Introduction Prognostic factors for functional outcome after basilar artery occlusion (BAO) treated with modern endovascular therapy (EVT) are sparse. We investigated the association between clinical characteristics, readily available imaging variables, and outcome in BAO patients treated with EVT. Methods Retrospective analysis from a large healthcare system’s prospectively collected code stroke registry of acute BAO patients treated with EVT between January 2017–January 2020. The primary outcome measure was a favorable 90-day modified Rankin score (mRS) of 0-2. Results 65 patients (median age 67 years, 57% male, median NIHSS 16) met the study inclusion criteria. Thrombolysis in Cerebral Infarction (TICI) 2 b-3 revascularization was achieved in 57/65 patients (88%) with a median time to revascularization of 445 minutes [IQR 302-840]. Ninety-day good outcome was seen in 35% (23/65) of patients. In a univariate analysis, age, history of ischemic stroke, baseline NIHSS, BAO site, and discharge mRS were associated with significant differences between the good and poor outcome groups. A multivariable logistic regression analysis demonstrated an independent association with 90-day good outcome and younger age (per 1-year, OR 0.79, 95% CI 0.64, 0.98) and good discharge mRS (0-2) (OR > 999.99, 95% CI 13.26, > 999.99). Conclusions Patients presenting with an acute BAO treated with modern EVT have a good 90-day outcome in over one-third of cases. Age and discharge mRS are independently associated with good 90-day outcome. Additional studies may focus on factors that can enhance discharge function after BAO, a novel prognostic indicator for favorable 90-day outcome in our study.