Primary brainstem hemorrhage (PBH) is one of the most fatal intracranial hemorrhages, evaluating the prognosis in the early stage is vital for appropriate therapeutic planning. Our study aimed to identify risk factors for 30-day mortality and 90-day functional recovery of PBH. Data from 63 patients with PBH admitted to Beijing Chaoyang Hospital between 2016 and 2022 were retrieved for this study. We grouped the patients according to 30-day survival or 90-day functional recovery. Independent risk factors of 30-day mortality and 90-day functional recovery were identified by univariate and multivariate logistic regression analyses. 31 patients (49.2%) died within 30 days and 22 patients (34.9%) achieved better functional recovery. By multivariate analysis, Glasgow coma scale <9 on admission and tachycardia were significantly associated with 30-day mortality, while the hematoma volume >5 mL was an independent risk factor for 90-day functional recovery. Initial level of consciousness, tachycardia, massive hematoma were risk factors for prognosis, which must be seriously evaluated for therapeutic planning.