Acute ischemic stroke due to basilar artery occlusion (BAO) carries a very poor prognosis. Functional outcomes in BAO patients undergoing endovascular therapy (EVT) may differ according to the specific pathological mechanisms. We aimed to explore the impact of the underlying pathological mechanisms on prognosis at 90-days and long-term follow-up in BAO patients treated with EVT. We analyzed consecutive BAO patients undergoing EVT from December 2012 to December 2018 at a single center (Xuanwu Hospital). Patients were classified into either an intracranial atherosclerotic disease (ICAD) group or an embolic group according to the corresponding angiographic findings. The baseline characteristics and functional outcomes were compared between the two groups. Multivariable logistic regression analysis was performed. Among the 167 patients enrolled, 78 patients (46.7%) were in the ICAD group and 89 patients (53.3%) were assigned to the embolic group. Ov erall, 149 patients (89.2%) achieved successful reperfusion post-EVT. There were no significant differences in functional outcomes at 90-days and long-term follow-up between the two groups. Similarly, a Kaplan-Meier survival analysis showed similar long-term survival probabilities (P = 0.438). The pathological mechanism was not associated with functional independence (OR, 1.818; 95% CI, 0.694-4.761; P = 0.224), favorable outcome (OR, 1.476; 95% CI, 0.592-3.681; P = 0.403), or mortality (OR, 1.249; 95% CI, 0.483-3.226; P = 0.646). However, based on subgroup analysis, embolic BAO versus ICAD was significantly associated with better functional independence in those aged 60 years and younger (OR, 4.513; 95% CI, 1.138-17.902). In this study, no differences in either 90days or long-term functional outcomes between ICAD-related BAO and embolic BAO patients undergoing EVT were observed. However, in BAO patients aged <= 60 years, the pathological mechanism of embolism was associated with better functional independence.