Flow diverter stent has been a promising device for intracranial aneurysm treatment. For treating aneurysms located in the anterior circulation, critical branches may be covered by flow diverter stent. The occlusion incidence of these branches has been reported, and even if branch vessel occlusions occur, associated neurological deficits are extremely rare. We present a 55-year-old woman who had a large saccular aneurysm at the right internal carotid artery (ICA). A developed fetal-type posterior communicating artery (PCOM) originated from the sac. We administered flow diverter stent deployment with coil insertion following surgical anastomosis of the superficial temporal artery to the posterior cerebral artery (STA-PCA) with ligation of the origin of the PCOM. On the seventh morning following the intervention, ischemic complication developed due to anterior choroidal artery occlusion jailed by the flow diverter stent. The occlusion of anterior choroidal artery covered by flow diverter stent is extremely rare. However, if the branch arises from the aneurysm sac, occlusion can transpire and induce serious complication. The most probable cause of occlusion in this case was that the orifice was jailed apart from the stent strut because the branch originated from the sac rather than the neck. Furthermore, the progression rate of intra-aneurysm thrombus formation is also an important factor affecting the side branch occlusion.