Neurodivergent students exhibit an inclination towards Science, Technology, Engineering and Mathematics (STEM) fields, yet their learning experiences in STEM courses remain underexamined. Utilizing an online survey of neurodivergent (n = 60) and neurotypical (n = 83) US college students, this study identified various factors influencing their self-perceived learning experiences, including interest in the course content, instruction quality and performance outcomes. Compared to their neurotypical peers, neurodivergent students attributed negative experiences in STEM courses less frequently to performance-related factors and more often to a mismatch between their interests and the course content. Both groups also articulated a variety of strengths and challenges encountered in their STEM studies. Neurodivergent students were more likely to report having interest and passion for STEM and less likely to report having peer support and effective study skills and habits as their primary strength for studying STEM. Conversely, while neurotypical students cited difficult content as their central challenge, neurodivergent students more commonly faced challenges with focus and attention. Despite the study's limited sample size, it revealed emerging patterns that emphasize the importance of developing inclusive teaching methods and specific support mechanisms to cater to the unique strengths and challenges of neurodivergent students in higher education.