Although the efficacy of mechanical thrombectomy (MT) for acute basilar artery occlusion (ABAO) has been established in two randomized controlled studies, many patients have miserable clinical outcomes after MT for ABAO. Predicting severe disability prior to the procedure might be useful in determining the appropriateness of treatment interventions. Among the ABAO cases treated at 10 hospitals between July 2014 and December 2021, 144 were included in the study, all of whom underwent MRI before treatment. A miserable outcome was defined as a modified Rankin Scale (mRS) of 5–6 at 3 months. The associations between clinical, imaging, and procedural factors and miserable outcomes were evaluated. A miserable outcome was observed in 54 cases (37.5%). Multivariate analysis identified the National Institutes of Health Stroke Scale (NIHSS), transverse diameter of brainstem infarction, and symptomatic intracerebral hemorrhage as independent factors associated with miserable outcomes, with cutoff values of NIHSS 22 and transverse diameter of brainstem infarction 15 mm. Cases with a higher preoperative severity may result in miserable postoperative outcomes. Particularly, the transverse diameter of a brainstem infarction can be easily measured and serves as a useful criterion for determining treatment indications.