Two related drugs have been shown to shrink or stabilize subependymal giant cell tumors: rapamycin and everolimus. These both belong to the mTOR inhibitor class of immunosuppressants, and are both contraindicated in patients with severe infections.

Rapamycin showed efficacy in five cases of SEGA in TSC patients, shrinking their tumor volumes by an average of 65%. However, after the drug was stopped, the tumors regrew.

Everolimus, which has a similar structure as rapamycin, but with slightly increased bioavailability and shorter half-life, was studied in 28 patients with SEGA. There was a significant reduction in SEGA size in 75% of the patients, and a mild improvement in their seizures. Everolimus was approved for the treatment of SEGA by the US Food and Drug Administration (FDA) in October, 2010.

A NIH Consensus Conference report in 1999 recommends that any SEGA that is growing or causing symptoms should be surgically removed. Tumors are also removed in cases where a patient is suffering from a high seizure burden. If a tumor is rapidly growing or causing symptoms of hydrocephalus, deferring surgery may lead to vision loss, need for ventricular shunt, and ultimately death. Total removal of the tumor is curative.

Surgery to remove intraventricular tumors also carries risks of complications or death. Potential complications include transient memory impairment, hemiparesis, infection, chronic ventriculoperitoneal shunt placement, stroke, and death.