Aviation is an interdisciplinary subject that has influenced human development over the last century. Learning about aviation exposes students to principles of flight, language, earth science, aeronautical engineering, flight training and airmanship. In K-12 education, educators have started to encourage children to learn science, technology, engineering and mathematics (STEM) subjects via aviation-themed activities to develop future scientists and engineers. This study investigated upper primary students' motivations to learn STEM via engaging in flight simulation experiences. The sample consisted of 345 10- to 13-year-old Hong Kong students from 8 primary schools. A modified version of the 31-item Science Motivation Questionnaire II (SMQ II) with four subscales with a focus on aviation was used. The relationships between intrinsic motivation, extrinsic motivation, self-efficacy and peer support across gender and performance were examined. The data obtained were analysed using factor analysis and a regression model. According to our model, students are most strongly motivated by peer support, followed by intrinsic motivation, and they are least motivated by self-efficacy. As expected, our results indicate that a gender gap exists in aviation-themed STEM learning. These findings can help educators to better understand students' perceptions of aviation science and further develop related learning activities.