The main treatment for isolated epispadias is a comprehensive surgical repair of the genito-urinary area usually during the first 7 years of life, including reconstruction of the urethra, closure of the penile shaft and mobilisation of the corpora. The most popular and successful technique is known as the modified Cantwell-Ransley approach. In recent decades however increasing success has been achieved with the complete penile disassembly technique despite its association with greater and more serious risk of damage.

The principal treatment of chordee is surgery in infancy, usually by a pediatric urologist. With chordees caused by circumcision, the preferred method of surgical treatment is a z-plasty. The preferred time for surgery is between the ages of 6 and 18 months and correction is usually successful.

Hormones potentially increase the size of the penis, and have been used in children with proximal hypospadias who have a smaller penis. Numerous articles report testosterone injections or topical creams increase the length and circumference of the penis. However, few studies discuss the impact of this treatment on the success of corrective surgery, with conflicting results. Therefore, the role, if any, for preoperative hormone stimulation is not clear at this time.

A problem for people with penile agenesis is the absence of a urinary outlet. Before genital metamorphosis, the urethra runs down the anal wall, to be pulled away by the genital tubercle during male development. Without male development this does not occur. The urethra can be surgically redirected to the rim of the anus immediately after birth to enable urination and avoid consequent internal irritation from urea concentrate. In such cases, the perineum may be left devoid of any genitalia, male or female.

A working penis transplant on to an agenetic patient has never been successful. Only one major penis graft was successfully completed. This occurred in China and the patient shortly rejected it on psychological grounds. However a full female or agenetic to male transplant is not yet facilitated to fulfil full reproductive functions.

On March 18, 2013, it was announced that Andrew Wardle, a British man born without a penis, was going to receive a pioneering surgery to create a penis for him. The surgeons hope to "fold a large flap of skin from his arm — complete with its blood vessels and nerves — into a tube to graft onto his pubic area." If the surgery goes well, the odds of starting a family are very good.

Hypospadias repair can be done in full-term, healthy infants at any time from 3 months of age. Premature babies generally have surgery done at 6 months or older. Using these guidelines, most babies can undergo repair as same-day surgery, without need to stay in the hospital afterwards.

The results of surgery are probably not influenced by the age at which repair is done, but older children are more likely to recall the event. Teens and adults typically spend one night in the hospital after surgery.

Even with successful surgery, patients may have long-term problems with:

- incontinence, where serious usually treated with some form of continent urinary diversion such as the Mitrofanoff

- depression and psycho-social complications

- sexual dysfunction

Because hormone treatment rarely achieves average size, several surgical techniques similar to phalloplasty for penis enlargement have been devised and performed; but they are not generally considered successful enough to be widely adopted and are rarely performed in childhood.

In extreme cases of micropenis, there is barely any shaft, and the glans appears to sit almost on the pubic skin. From the 1960s until the late 1970s, it was common for sex reassignment and surgery to be recommended. This was especially likely if evidence suggested that response to additional testosterone and pubertal testosterone would be poor. With parental acceptance, the boy would be reassigned and renamed as a girl, and surgery performed to remove the testes and construct an artificial vagina. This was based on the now-questioned idea that gender identity was shaped entirely from socialization, and that a man with a small penis can find no acceptable place in society.

Johns Hopkins Hospital, the center most known for this approach, performed twelve such reassignments from 1960 to 1980, most notably that of David Reimer (whose penis was destroyed by a circumcision accident), overseen by John Money. By the mid-1990s, reassignment was less often offered, and all three premises had been challenged. Former subjects of such surgery, vocal about their dissatisfaction with the adult outcome, played a large part in discouraging this practice. Sexual reassignment is rarely performed today for severe micropenis (although the question of raising the boy as a girl is sometimes still discussed.) (See "History of intersex surgery" for a fuller discussion.)

A treatment option for micropenis is the insertion of a subcutaneous soft silicone implant under the penile skin. The procedure was developed by urologist James J. Elist.

Congenital anomalies like cryptorchidism, renal agenesis/dysplasia, musculoskeletal and cardiopulmonary anomalies are also common (>50% cases), hence evaluation of the patient for internal anomalies is mandatory.

Although aphallia can occur in any body type, it is considered a substantially more troublesome problem with those who have testes present, and has in the past sometimes been considered justification for assigning and rearing a genetically male infant as a girl. After the theory in the 1950s that gender as a social construct was purely nurture and so an individual child could be raised early on and into one gender or the other regardless of their genetics or brain chemistry. Intersex people generally advocate harshly against coercive genital reassignment however, and encourage infants to be raised choosing their own gender identity. The nurture theory has been largely abandoned and cases of trying to rear children this way have not proven to be successful transitions.

In newborn period or infancy, feminizing operations are recommended for treatment of penile agenesis, but after 2 years, as sexual identification of the patients has appeared, it is advised to perform masculinizing operations in order not to disturb the child psychologically.

Recent advances in surgical phalloplasty techniques have provided additional options for those still interested in pursuing surgery.

Growth of the penis both before birth and during childhood and puberty is strongly influenced by testosterone and, to a lesser degree, the growth hormone. However, later endogenous hormones mainly have value in the treatment of micropenis caused by hormone deficiencies, such as hypopituitarism or hypogonadism.

Regardless of the cause of micropenis, if it is recognized in infancy, a brief course of testosterone is often prescribed (usually no more than 3 months). This usually induces a small amount of growth, confirming the likelihood of further growth at puberty, but rarely achieves normal size. No additional testosterone is given during childhood, to avoid unwanted virilization and bone maturation. (There is also some evidence that premature administration of testosterone can lead to reduced penis size in the adult.)

Testosterone treatment is resumed in adolescence only for boys with hypogonadism. Penile growth is completed at the end of puberty, similar to the completion of height growth, and provision of extra testosterone to post-pubertal adults produces little or no further growth.

When an infant is born with PSH, the most difficult management decision has often been the sex assignment, since genitalia with this degree of ambiguity do not resemble either sex very well with respect to looks or function. Many infants with PPHS have been assigned and raised as female despite presence of testes and XY chromosomes.

Nearly all parents of infants with PPSH are offered surgical reconstruction, to either further masculinize or feminize the external genitalia.

Treatment with testosterone postnatally does not close the urethra or change the malformation, but in some cases may enlarge the penis slightly.

Paraphimosis can be avoided by bringing the foreskin back into its normal, forward, non-retracted position after retraction is no longer necessary (for instance, after cleaning the glans penis or placing a Foley catheter). Phimosis (both pathologic and normal childhood physiologic forms) is a risk factor for paraphimosis; "physiologic" phimosis resolves naturally as a child matures, but it may be advisable to treat "pathologic" phimosis via long-term stretching or elective surgical techniques (such as preputioplasty to loosen the preputial orifice or circumcision to amputate the foreskin tissue partially or completely).

The foreskin responds to the application of tension to cause expansion by creating new skin cells though the process of mitosis. The tissue expansion is permanent. Non-surgical stretching of the foreskin may be used to widen a narrow, non-retractable foreskin. Stretching may be combined with the use of a steroid cream. Beaugé recommends manual stretching for young males in preference to circumcision as a treatment for non-retractile foreskin because of the preservation of sexual sensation.

Paraphimosis can often be effectively treated by manual manipulation of the swollen foreskin tissue. This involves compressing the glans and moving the foreskin back to its normal position, perhaps with the aid of a lubricant, cold compression, and local anesthesia as necessary. If this fails, the tight edematous band of tissue can be relieved surgically with a dorsal slit or circumcision. An alternative method, the Dundee technique, entails placing multiple punctures in the swollen foreskin with a fine needle, and then expressing the edema fluid by manual pressure. According to Ghory and Sharma, treatment by circumcision may be elected as "a last resort, to be performed by a urologist". Other experts recommend delaying elective circumcision until after paraphimosis has been resolved.

Surgical methods range from the complete removal of the foreskin to more minor operations to relieve foreskin tightness:

- Dorsal slit (superincision) is a single incision along the upper length of the foreskin from the tip to the corona, exposing the glans without removing any tissue.

- Ventral slit (subincision) is an incision along the lower length of the foreskin from the tip of the frenulum to the base of the glans, removing the frenulum in the process. Often used when frenulum breve occurs alongside the phimosis.

- Preputioplasty, in which a limited dorsal slit with transverse closure is made along the constricting band of skin, can be an effective alternative to circumcision. It has the advantage of only limited pain and a short time of healing relative to circumcision, and avoids cosmetic effects.

- Circumcision is sometimes performed for phimosis, and is effective, but this was becoming less common as of 2012.

While circumcision prevents phimosis, studies of the incidence of healthy infants circumcised for each prevented case of phimosis are inconsistent.

The FDA does not recommend alternative therapies to treat sexual dysfunction. Many products are advertised as "herbal viagra" or "natural" sexual enhancement products, but no clinical trials or scientific studies support the effectiveness of these products for the treatment of erectile dysfunction, and synthetic chemical compounds similar to sildenafil have been found as adulterants in many of these products. The United States Food and Drug Administration has warned consumers that any sexual enhancement product that claims to work as well as prescription products is likely to contain such a contaminant.

The PDE5 inhibitors sildenafil (Viagra), vardenafil (Levitra) and tadalafil (Cialis) are prescription drugs which are taken orally.

A cream combining alprostadil with the permeation enhancer DDAIP has been approved in Canada as a first line treatment for erectile dysfunction.

One of the following medications maybe injected into the penis: papaverine, phentolamine, and prostaglandin E1.

Physiologic phimosis, common in males 10 years of age and younger, is normal, and does not require intervention. Non-retractile foreskin usually becomes retractable during the course of puberty.

If phimosis in older children or adults is not causing acute and severe problems, nonsurgical measures may be effective. Choice of treatment is often determined by whether circumcision is viewed as an option of last resort to be avoided or as the preferred course.

The condition may be treated with surgery. There are several different techniques to treat this condition. Threading a suture through the lower membrane, and then tying a tight knot around the frenulum itself is a procedure that minimises invasive action. After a few days the frenulum will weaken and eventually break apart to allow the prepuce to fully retract. Other procedures involve the cutting of the skin and require the use of sutures to help in the healing process. Stretching exercises and steroid creams may also be helpful. Alternatively, it may be treated by a reparative plastic surgery operation called a frenuloplasty, or by complete circumcision including resection of the frenulum (frenectomy).

A bifid penis (or double penis) is a rare congenital defect where two genital tubercles develop.

Historically, males born with a bifid penis often underwent sex reassignment surgery, due to the difficulty of penile reconstruction. They were raised as girls, and often had reconstructive surgery to make them phenotypically female, coupled with female hormone replacement therapy. However, in recent years, this practice has fallen under heavy scrutiny due to both a high frequency of sexual dysfunction in gender converted children, and more advanced penile reconstruction techniques.

Many male marsupials naturally have a bifid penis, with left and right prongs that they insert into multiple vaginal canals simultaneously.

Pseudovaginal perineoscrotal hypospadias (PPSH) refers to a configuration of the external genitalia of an infant. In a sense, this configuration is roughly midway between normal male genitalia and normal female genitalia in structure and appearance. It is a relatively common form of genital ambiguity caused by undervirilization of genetic males due to several different intersex conditions.

Penile fracture is a medical emergency, and emergency surgical repair is the usual treatment. Delay in seeking treatment increases the complication rate. Non-surgical approaches result in 10–50% complication rates including erectile dysfunction, permanent penile curvature, damage to the urethra and pain during sexual intercourse, while operatively treated patients experience an 11% complication rate.

In some cases, retrograde urethrogram may be performed to rule out concurrent urethral injury.

Many oral treatments have been studied, but results so far have been mixed. Some consider the use of nonsurgical approaches to be "controversial".

Collagenase clostridium histolyticum (marketed as Xiaflex by [Auxilium]), a drug originally approved by the FDA to treat Dupuytren's contracture, is now an FDA-approved injectable drug for treatment of Peyronie's disease. The drug is reported to work by breaking down the excess collagen in the penis that causes Peyronie's disease.

Vitamin E supplementation has been studied for decades, and some success has been reported in older trials, but those successes have not been reliably repeated in larger, newer studies. A combination of Vitamin E and colchicine has shown some promise in delaying progression of the condition.

Some newer agents targeting the basic mechanisms of inflammation have been studied in larger clinical trials. These include potassium para-aminobenzoate (Potaba), pentoxifylline (acting through TGFβ1 inhibition), and Coenzyme Q10.

The efficacy of Interferon-alpha-2b in the early stages of the disease has been reported in recent publications, but it was found to be less effective in cases where calcification of the plaque had occurred in common with many treatments.

Aphallia is a congenital malformation in which the phallus (penis or clitoris) is absent. It is the female counterpart of penile agenesis and testicular agenesis. The word is derived from the Greek "a-" for "not", and "phallos" for "penis". It is classified as an intersex condition.

Although there are no approved pharmaceuticals for addressing female sexual disorders, several are under investigation for their effectiveness. A vacuum device is the only approved medical device for arousal and orgasm disorders. It is designed to increase blood flow to the clitoris and external genitalia. Women experiencing pain with intercourse are often prescribed pain relievers or desensitizing agents. Others are prescribed lubricants and/or hormone therapy. Many patients with female sexual dysfunction are often also referred to a counselor or therapist for psychosocial counseling.

Webbed penis, also called penis palmatus or penoscrotal fusion, is an acquired or congenital condition in which the scrotal skin extends onto the ventral penile shaft. The penile shaft is buried in scrotum or tethered to the scrotal midline by a fold or web of skin. The urethra and erectile bodies are usually normal. Webbed penis is usually asymptomatic, but the cosmetic appearance is often unacceptable. This condition may be corrected by surgical techniques.

In the congenital form, the deformity represents an abnormality of the attachment between the penis and the scrotum; the penis, the urethra, and the remainder of the scrotum typically are normal.

Webbed penis may also be acquired (iatrogenic) after circumcision or other penile surgery, resulting from excessive removal of ventral penile skin; the penis can retract into the scrotum, resulting in secondary phimosis (trapped penis).

One procedure for webbed penis is the insertion of a subcutaneous soft silicone implant under the penile skin. The procedure was developed by urologist James J. Elist.

Surgery, such as the "Nesbit operation" (which is named after Reed M. Nesbit (1898–1979), an American urologist at University of Michigan), is considered a last resort and should only be performed by highly skilled urological surgeons knowledgeable in specialized corrective surgical techniques. A penile prosthesis may be appropriate in advanced cases.

The type of injury dictates the treatment; however, surgery is a common treatment. Catheterization is usually a part of treatment for penis injuries; when the urethra is intact, urethral catheterization may be used, but if it has been injured, suprapubic catheterization is used. Some injuries, including animal bites, are also treated with antibiotics, irrigation, and rabies prophylaxis.