Background: This study aimed to evaluate and compare the neurocognitive outcomes of adult quasi-moyamoya disease (quasi-MMD) patients with autoimmune diseases (AIDs) to help better manage these patients. Methods: We performed a structured battery of neurocognitive tests to analyze and compare the neurocognitive outcomes of adult quasi-MMD patients with AID in our hospital from October 2000 to September 2015. Results: Overall, 27.3% of the neuropsychological test comparisons indicated a significant improvement in cognition, and a significant decline was found in 6%. In 47.4% of comparisons, the observed difference did significantly change the reliable change indices (RCI) before and after anti-autoimmune treatment. We found that the number of patients showing significant improvements, and no change in cognitive outcomes did differ between quasi-MMD and MMD (31.8% vs 14.9% with p = 0.006 and 50.0% vs 66.8% with p = 0.031, respectively; Chi-squared test). The incidence of cognitive decline in quasi-MMD patients (18.2%) did not significantly differ from that in MMD patients (18.3%) (p = 0.982). After adjusting for covariates, including sex, age, type 2 diabetes mellitus, risk factors, other comorbidities, and AID, multiple logistic regression analysis suggested that AID was more likely to aggravate the neurocognitive outcome of quasi-MMD patients (p = 0.042, odds ratio (OR) 6.78, 95% confidence interval (CI) 1.31-62.71). Conclusions: AID was more likely to aggravate the neurocognitive outcome of quasi-MMD patients, and anti-autoimmune treatment could improve long-term neurocognitive outcomes. These findings indicated that AID seemed to be an independent risk factor for the pathological and physiological mechanisms of quasi-MMD.