Objective: We aimed to identify unfavorable prognostic factors for the development of cerebral ischemic complications of surgical treatment in patients with moyamoya disease. Methods: We analyzed 80 patients with moyamoya disease, who underwent 134 surgical revascularizations. Persistent complications (ischemic strokes) developed in seven cases (5.3%). In 36 cases (27%), there were short-term episodes of transient neurologic deficit. Results: The statistical analysis revealed factors associated with the development of transient and persistent ischemic complications: neuroradiological “ivy sign” (χ2 = 4.078, p = 0.043), stenosis of the ICA proximal to the PComA or PCA (χ2 = 20.085, p < 0.0001), decompensation of cerebral blood flow (χ2 = 11.212, p < 0.001), recent CVA (less than 3 months before surgery) or instability of neurological symptoms (χ2 = 6.146, p < 0.013). Significant factors of the development of persistent ischemic stroke were as follows: stenosis or occlusion of the ipsilateral PCA (increasing the risk of stroke by 9.7 times); signs of the decompensation of cerebral perfusion (increased risk by 5.4 times); and unstable clinical symptoms within 3 months before surgery (increased risk by 6.4 times). The presence of at least two signs defines a group of patients that has an increased risk of complications with a sensitivity of 80.7% and a specificity of 88.6%. Conclusion: The identified risk factors will enable predicting the risk of perioperative ischemic complications in patients with moyamoya disease and optimize management tactics and improve the results of surgical treatment.