This study reports our experience with the endovascular treatment of basilar artery (BA) trunk and branch aneurysms. Subjects included 16 patients with BA trunk and branch aneurysms who underwent endovascular treatment in our hospital from October 2000 to October 2009, including four patients with associated arteriovenous malformation (AVM), two with associated moyamoya disease, one with multiple aneurysms at adjacent sites, and one with a distant aneurysm. Endovascular coil embolization, together with stent or balloon assistance when necessary, or while occluding the parent artery was performed. Associated diseases were managed intraoperatively or in the second stage, or treated with gamma knife radiotherapy, or followed up. Two patients with unsuccessful embolization died of re-rupture at the fourth month and fifth month follow-up. The remaining 14 patients reported good outcomes and experienced no re-rupture of either the aneurysm or associated disease. Angiographic follow-ups were conducted for the 14 patients for six to 12 months. Digital subtraction angiography (DSA) examination at the last follow-up showed no recurrence of the BA trunk and branch aneurysms. Together, BA trunk and branch aneurysms should be actively managed via endovascular techniques to prevent serious consequences due to aneurysm rupture and bleeding. Favorable outcomes can be obtained by the proper selection of endovascular treatment regimens.