The natural history of this disorder is not well known. Symptomatic Moyamoya disease have occurred in individuals with seemingly asymptomatic stability thought due to vascular insufficiency secondary to brain trauma which may result from axonal shearing and acceleration / deceleration injuries such as falls and/or high speed motor vehicle accidents.

The long term outlook for patients with treated moyamoya seems to be good. While symptoms may seem to improve almost immediately after the in-direct EDAS, EMS, and multiple burr holes surgeries, it will take probably 6–12 months before new vessels (blood supply) can develop sufficiently. With the direct STA-MCA surgery, increased blood supply is immediate. Once major strokes or bleeding take place, even with treatment, the patient may be left with permanent loss of function so it is very important to treat this condition promptly.