Few studies have investigated the association between plasma Homocysteine (Hcy) levels in patients with recanalization after acute Basilar Artery Occlusion (BAO). This study investigated the predictive value of Hcy on the clinical prognosis of patients with recanalization after acute BAO. Altogether, 829 participants were recruited from the standard medical treatment plus endovascular treatment group of the Acute Basilar Artery Occlusion Study (BASILAR). Hcy levels were measured the morning after admission. The primary outcome was a combination of death and major disability (modified Rankin Scale score 4-6) at 90 days, and the secondary outcome was the mortality of patients with recanalization after acute BAO within 90 days. We used multivariable logistic regression modeling to estimate the association between Hcy and prognosis in our participants at 90 days. Altogether, 647 patients were assessed, and 302 patients were included in this study. The median was 12.88 μmol/L, and the mean Hcy concentration was 15.49 μmol/L. Elevated plasma Hcy levels (Hcy >12.88 μmol/L) were associated with poor functional outcomes (adjusted odds ratio 1.922, 95% confidence interval (CI) 1.048-3.528, P=0.035), but not with mortality (adjusted odds ratio 1.605, 95% CI 0.986-2.489, P=0.058). In further subgroup analysis, the conclusion was consistent in all predefined subgroups. Our analysis suggests that elevated plasma Hcy levels have a predictive value for functional outcomes in patients with recanalization after acute BAO during the 90-day follow-up period, but not for mortality.