Objective To explore the correlation between the serum folate level and the 3-month functional outcomes of small vessel disease in ischemic stroke patients. Methods A total of 83 ischemic stroke patients classified in small vessel disease admitted in the Department of Neurology of Haidian Hospital consecutively from 1st January to 30th September 2018， were enrolled. The clinical data， including age， gender， cerebrovascular risk factors， National Institute of Health stroke scale （NIHSS） score，complications during hospitalization and antithrombotic therapy during hospitalization were analyzed. According to the modified Rankin Scale （mRS）， the patients were divided into the group with good prognosis （mRS ≥ 3） （51 cases） and the group with poor prognosis （mRS ＜ 3） （32 cases）. The differences of the clinical data and serum folate concentrations were compared between the two groups. The fasting venous blood was collected to measure the serum folate level. Binary logistic regression was used to estimate the independentriskfactorsfor poor prognosis. Results The NIHSS scores of patients in poor prognosis group ［4.0（3.0，6.0）］were significantly higher than those in good prognosis group ［3.0（2.0，4.0）］（Z=-2.951，P=0.003）. The serum levels of folate in poor prognosis group ［11.3（9.9，16.7）μg/L］ were lower than those in good prognosis group ［15.6（11.5，22.8）μg/L］（Z=2.732， P=0.006）. Binary logistic analysis showed that increased NIHSS wastheindependentriskfactor for poorprognosis （OR=1.525， 95%CI=1.043-2.231， P=0.030）， while elevated serumfolateconcentration was an independent influence factor for goodprognosis （OR=0.729， 95%CI=0.554-0.960， P=0.024）. Conclusions Elevated serum folate level is an independent protective factor for poor functional prognosis.