The flow diverter is becoming a standard device for treating cerebral aneurysms. The aim of this in vitro study was to evaluate the impact of flow complexity on the effectiveness of flow diverter stents in a cerebral aneurysm model. The flow pattern of a carotid artery was decomposed into harmonics to generate four flow patterns with different pulsatility indexes ranging from 0.72 to 1.44. The effect of flow diverters on the aneurysm was investigated by injecting red dye or erythrocytes as markers. The recorded images were postprocessed to evaluate the maximum filling of the aneurysm cavity and the washout time. There were significant differences in the cut-off flows between the markers, linked to the flow complexity. Increasing the pulsatility index altered the performance of the flow diverter. The red dye was more sensitive to changes in flow than the red blood cell markers. The flow cut-off depended on the diverter design and the diverter deployment step was crucial for reproducibility of the results. These results strongly suggest that flow complexity should be considered when selecting a flow diverter.