An internal septum within a basilar artery aneurysm is an infrequent anomaly and is very rarely reported in the literature. We report a 62-year-old lady that was incidentally diagnosed with basilar tip aneurysm. Further imaging with magnetic resonance imaging (MRI) revealed internal septation within this aneurysm which was later confirmed with digital subtraction angiography (DSA). She underwent coil embolisation, which involved technical manipulation of the microcatheter and the balloon to enable coiling of each separate aneurysm compartment. We present this case to illustrate the effect of this anatomical variation on the selection of endovascular treatment strategy.