A lumbar puncture is a procedure in which cerebral spinal fluid is removed from the spine with a needle. A lumbar puncture is necessary to look for infection or blood in the spinal fluid. A lumbar puncture can also evaluate the pressure in the spinal column, which can be useful for people with idiopathic intracranial hypertension (usually young, obese women who have increased intracranial pressure), or other causes of increased intracranial pressure. In most cases, a CT scan should be done first.

All people who present with red flags indicating a dangerous secondary headache should receive neuroimaging. The best form of neuroimaging for these headaches is controversial. Non-contrast computerized tomography (CT) scan is usually the first step in head imaging as it is readily available in Emergency Departments and hospitals and is cheaper than MRI. Non-contrast CT is best for identifying an acute head bleed. Magnetic Resonance Imaging (MRI) is best for brain tumors and problems in the posterior fossa, or back of the brain. MRI is more sensitive for identifying intracranial problems, however it can pick up brain abnormalities that are not relevant to the person's headaches.

The American College of Radiology recommends the following imaging tests for different specific situations:

Cluster headaches are often misdiagnosed, mismanaged, or undiagnosed for many years; they may be confused with migraine, "cluster-like" headache (or mimics), CH subtypes, other TACs ( trigeminal autonomic cephalalgias), or other types of primary or secondary headache syndrome. Cluster-like head pain may be diagnosed as secondary headache rather than cluster headache.

A detailed oral history aids practitioners in correct differential diagnosis, as there are no confirmatory tests for CH. A headache diary can be useful in tracking when and where pain occurs, how severe it is, and how long the pain lasts. A record of coping strategies used may help distinguish between headache type; data on frequency, severity and duration of headache attacks are a necessary tool for initial and correct differential diagnosis in headache conditions.

Correct diagnosis presents a challenge as the first CH attack may present where staff are not trained in the diagnosis of rare or complex chronic disease. Although experienced ER staff are sometimes trained to detect headache types, CH attacks themselves are not directly life-threatening, they are linked to an increased risk of suicide.

Individuals with CH typically experience diagnostic delay before correct diagnosis. People are often misdiagnosed due to reported neck, tooth, jaw, and sinus symptoms and may unnecessarily endure many years of referral to ear, nose and throat (ENT) specialists for investigation of sinuses; dentists for tooth assessment; chiropractors and manipulative therapists for treatment; or psychiatrists, psychologists and other medical disciplines before their headaches are correctly diagnosed. Under-recognition of CH by health care professionals is reflected in consistent findings in Europe and the United States that the average time to diagnosis is around seven years. Medical students receive little training in differential diagnoses and management of headaches.

Cluster headache may be misdiagnosed as migraine or sinusitis. Other types of headache are sometimes mistaken for, or may mimic closely, CH. Incorrect terms like "cluster migraine" confuse headache types, confound differential diagnosis and are often the cause of unnecessary diagnostic delay, ultimately delaying appropriate specialist treatment.

Headaches that may be confused with CH include:

- Chronic paroxysmal hemicrania (CPH) is a unilateral headache condition, without the male predominance usually seen in CH. Paroxysmal hemicrania may also be episodic but the episodes of pain seen in CPH are usually shorter than those seen with cluster headaches. CPH typically responds "absolutely" to treatment with the anti-inflammatory drug indomethacin where in most cases CH typically shows no positive indomethacin response, making "Indomethacin response" an important diagnostic tool for specialist practitioners seeking correct differential diagnosis between the conditions.

- Short-lasting unilateral neuralgiform headache with conjunctival injection and tearing (SUNCT) is a headache syndrome belonging to the group of TACs.

- Trigeminal neuralgia is a unilateral headache syndrome, or "cluster-like" headache.

Preventive treatments of migraines include medications, nutritional supplements, lifestyle alterations, and surgery. Prevention is recommended in those who have headaches more than two days a week, cannot tolerate the medications used to treat acute attacks, or those with severe attacks that are not easily controlled.

The goal is to reduce the frequency, painfulness, and/or duration of migraines, and to increase the effectiveness of abortive therapy. Another reason for prevention is to avoid medication overuse headache. This is a common problem and can result in chronic daily headache.

Long term prognosis in people with migraines is variable. Most people with migraines have periods of lost productivity due to their disease; however typically the condition is fairly benign and is not associated with an increased risk of death. There are four main patterns to the disease: symptoms can resolve completely, symptoms can continue but become gradually less with time, symptoms may continue at the same frequency and severity, or attacks may become worse and more frequent.

Migraines with aura appear to be a risk factor for ischemic stroke doubling the risk. Being a young adult, being female, using hormonal birth control, and smoking further increases this risk. There also appears to be an association with cervical artery dissection. Migraines without aura do not appear to be a factor. The relationship with heart problems is inconclusive with a single study supporting an association. Overall however migraines do not appear to increase the risk of death from stroke or heart disease. Preventative therapy of migraines in those with migraines with auras may prevent associated strokes. People with migraines, particularly women, may develop higher than average numbers of white matter brain lesions of unclear significance.

As diagnostic criteria have been indecisive and its pathophysiology remains unclear, no permanent cure is available. Antiepileptic medications (membrane-stabilizing drugs) such as pregabalin, gabapentin, topiramate, and lamotrigine improve symptoms, but there is no effective permanent or long-term treatment for SUNCT.

However, a few short-term treatments are available and can relieve and possibly prevent some symptoms of attacks.

Lamotrigine exhibits some long-term prevention and reduction in many patients; however, titration of dose is difficult due to adverse skin reactions.

Topiramate also has preventive effects but it is accompanied by a high risk of severe side-effects for patients with a history of kidney stones, glaucoma, depression, or low body weight.

Intravenous lidocaine can abolish symptoms during its administration, or reduce frequency and duration of attacks. However, administration of intravenous lidocaine requires careful monitoring of ECG and blood pressure.

Methylprednisolone therapy shows some promise in short-term prevention of attacks, even though its mechanism of action is yet to be discovered.

The calcium channel blocker verapamil is reported to be useful in alleviating symptoms (lower frequency and duration of attacks), even though some patients experience worsened symptoms.

Various medications that are often used in other headache syndromes such as nonsteroidal anti-inflammatory drugs, acetaminophen, tricyclic antidepressants, calcium channel antagonists do not relieve the symptoms of SUNCT.

There have been attempts to alter oxygen supply during attacks to alleviate the symptoms since some of the headaches are caused by decreased oxygen supply; however, elevated blood oxygen level did not affect the symptoms.

Researchers now focus on the administration of various combination of medications and therapies to treat symptoms of SUNCT.

SUNCT must be properly distinguished from cluster headaches, since cluster headaches also occur several times per day with separate attacks, and share some common symptoms. However, cluster headaches usually last longer (up to three hours), occur less often (three to five attacks per day), and do not accompany cranial autonomic symptoms. IHS standard criteria for the diagnosis of SUNCT specifically includes pain in the trigeminal division of the face, especially in the orbital region, often with cranial autonomic symptoms which last for relatively short periods of time (from five seconds to several minutes) up to 100 times per day. SUNCT is a major subset of SUNA, which does not accompany cranial symptoms; complete separation between the two is inappropriate since SUNCT does not necessarily always accompany cranial autonomic signs. Exact statistical data is not available due to common mis-diagnosis, and setting up diagnostic criteria is important.

The International Headache Classification established by the International Headache Society criteria for diagnosing SUNCT for therapeutic purposes is:

Symptoms of SUNCT often lead to misdiagnosis as paroxysmal hemicrania, which is also categorized in the same group. Inefficiency of indomethacin usually indicates SUNCT over paroxysmal hemicrania.

Misdiagnosis and indecisive diagnosis in the past has made it difficult to obtain accurate statistics about SUNCT. Proper diagnosis will broaden data availability and facilitate discovery of new treatment options and useful statistics.

A physician may recommend engaging in sexual activity less strenuously. Case series have found indomethacin and beta blockers to be successful in treating these headaches. Propranolol, Bellergal, and triptans have also been used with success. Anecdotal and indirect evidence suggests a trial of magnesium supplementation may improve symptoms (in subjects with known or suspected low Mg levels).

These headaches are estimated to appear in roughly 1% of the population. They can occur with sexual activity at any age. It is more common in men than women, with studies putting the gender ratio between 1.2:1 and 3:1.

Cephalalgiaphobia is fear of headache, or fear of the next headache. It is derived from "cephalalgia" and "phobia". The term is used for patients that are fearful of headache pain, or even exhibiting pain-panic. Cephalgiaphobia is a psychological state and has been linked to producing and also continuing the overuse of medication. "Pain-panic" situation is described as a significant and uncontrolled fear over anticipated painful events, which can prompt excessive and obsessive drug-taking behavior and, ultimately, medication overuse. The medication overuse may turn, in turn, itself be the cause medication overuse headache. The term cephalgiaphobia was coined by Dr. Harvey Featherstone in the mid-1980s