Background Intracranial aneurysms are increasingly being treated by the placement of flow diverters; however, the factors affecting the outcome of aneurysms treated using flow diverters remain unclarified. Methods The present study investigated 94 aneurysms treated with pipeline embolisation device placement, and used a computational fluid dynamics method to explore the factors influencing the outcome of aneurysms. Results Seventy-six completely occluded aneurysms and 18 incompletely occluded aneurysms were analysed. Before treatment, inflow jets were found in 13 (72.2%) aneurysms in the incompletely occluded group and 34 (44.7%) in the completely occluded group ( P = 0.292). After deployment of the pipeline embolisation device, inflow jets remained in nine (50%) aneurysms in the incompletely occluded group and nine (11.8%) in the completely occluded group ( P = 0.001). In the incompletely occluded group, regions with inflow jets after treatment corresponded with the patent areas shown on follow-up digital subtraction angiography. The mean reduction ratios of velocity in the whole aneurysm and on the neck plane were lower in the incompletely occluded than in the completely occluded group ( P = 0.003; P = 0.017). Multivariate analysis revealed that the only independent risk factors for incomplete aneurysm occlusion were the reduction ratios of velocity (in the whole aneurysm, threshold 0.362, P = 0.005; on the neck plane, threshold 0.273, P = 0.015). Conclusions After pipeline embolisation device placement, reduction ratios of velocity in the whole aneurysm of less than 0.362 and on the neck plane of less than 0.273 are significantly associated with a greater risk of aneurysm incomplete occlusion. In addition, the persistence of inflow jets in aneurysms is associated with incomplete occlusion in the inflow jet area.