Background Data on outcome after endovascular treatment of basilar artery fenestration aneurysms (BAFAs) is limited. This study presents our multi-centre experience of BAFAs treated by different reconstructive techniques including coils, stent-assisted coiling (SAC), flow diversion and intra-saccular flow disruption with the Woven Endobridge (WEB). Methods Retrospective analysis of 38 BAFAs treated endovascularly between 2003 and 2020. The primary endpoint was complete aneurysm obliteration defined as Raymond–Roy occlusion classification (RROC) I on immediate and follow-up (FU) angiography. The secondary endpoints were procedure-related complications, rate of re-treatment, and clinical outcome. Results Endovascular treatment was feasible in 36/38 aneurysms (95%). The most frequent strategy was coiling (21/36, 58%), followed by SAC (7/36, 19%), WEB embolization (6/36, 17%) and flow diversion (2/36, 6%). A successful aneurysm occlusion (defined as RROC 1 and 2) on the final angiogram was achieved in 30/36 (83%) aneurysms including all patients presenting with baseline subarachnoid haemorrhage and 25/36 (69%) were occluded completely. Complete occlusion (RROC 1) was more frequently achieved in ruptured BAFAs (15/25, 60% v. 2/11, 18%; p = 0.031). Procedure-related complications occurred in 3/36 (8%) aneurysms. Re-treatment was executed in 12/36 (33%) aneurysms. After a median angiography FU of 38 months, 30/31 (97%) BAFAs were occluded successfully and 25/31 (81%) showed complete occlusion. Conclusion Reconstructive endovascular treatment of BAFAs is technically feasible with a good safety profile. Although in some cases re-treatment was necessary, a high rate of final aneurysm occlusion was achieved.