Background Basilar thrombosis frequently leads to poor functional outcomes, even with good endovascular reperfusion. We studied factors associated with severe disability or death in basilar thrombectomy patients achieving revascularization. Methods We retrospectively analyzed records from a health system's code stroke registry, including successful basilar thrombectomy patients from January 2017 to May 2023 who were evaluated with pretreatment computed tomography perfusion. The primary outcome was devastating functional outcome (90-day modified Rankin Scale [mRS] score 5–6). A multivariable logistic regression model was constructed to determine independent predictors of the primary outcome. The area under the receiver operator characteristics curve (AUC) was calculated for the model distinguishing good from devastating outcome. Results Among 64 included subjects, with mean (standard deviation) age 65.6 (14.1) years and median (interquartile range) National Institutes of Health Stroke Scale (NIHSS) 18 (5.75–24.5), the primary outcome occurred in 28 of 64 (43.8%) subjects. Presenting NIHSS (odds ratio [OR] 1.08, 95% confidence interval [CI] 1.01–1.14, p = 0.02), initial glucose (OR 0.99, 95% CI 0.97–1.00, p < 0.05), and proximal occlusion site (OR 7.38, 95% CI 1.84–29.60, p < 0.01) were independently associated with 90-day mRS 5–6. The AUC for the multivariable model distinguishing outcomes was 0.81 (95% CI 0.70–0.92). Conclusion We have identified presenting stroke severity, lower glucose, and proximal basilar occlusion as predictors of devastating neurological outcome in successful basilar thrombectomy patients. These factors may be used in medical decision making or for patient selection in future clinical trials.