Fighter pilots may be exposed to extended flight missions. Consequently, there is increasing concern about fatigue. We investigated the effects of fatigue and cognitive performance in a simulated 11-hr mission in the 39 Gripen fighter aircraft. Five cognitive tasks were used to assess cognitive performance. Fatigue was measured with the Samn–Perelli Fatigue Index. Results showed that performance in the non-executive task degraded after approximately 7 hr. Fatigue ratings showed a matching trend to the performance in this task. Performance in tasks taxing executive functions did not decline. We interpreted that fatigue can be overridden by increased attentional effort for executive tasks but not for non-executive components of cognition. Participants underestimated their performance and metacognitive accuracy was not influenced by fatigue.