Spatial disorientation (SD) is one of the main causes of incidents and accidents in aviation. While most studies have investigated the effect of SD on the control task, we tested the effect of SD on cognitive performance in an operationally representative environment. Thirteen Dutch military helicopter pilots flew scenarios with six different SD events using an AH-64 Apache flight model in virtual reality in a 6-DoF motion simulator. The SD events used were: “False Horizon”, “Featureless Terrain”, “the Leans”, “Brownout”, “Somatogyral Illusion” and “Night Vision Goggles (NVGs)”. Corresponding scenarios without the SD events were performed to obtain baseline measures of cognitive performance. When performing the scenarios, participants had either the role of pilot flying or pilot monitoring. To test the cognitive performance, participants performed a mathematical processing task. The corrected reaction time and error rate were significantly higher during the SD events than during the baseline events. These effects were most prominent in the “Featureless Terrain” and “the Leans” scenarios. The results indicate that SD has a negative impact on the cognitive performance of military helicopter pilots. These findings underline the importance of SD awareness training for pilots, as well as the use of workload management procedures when experiencing SD.