The prevalence of underweight among young women is a serious international health issue. However, the evidence on how being underweight negatively affects brain health and cognition is still unclear. This study investigated the association between underweight status, academic performance, and neurocognitive control in young Japanese women using a cross-sectional design. We analyzed the academic performance of female undergraduates, comparing underweight and healthy weight groups (n = 43; age 18–23 years, M = 21.1, SD = 1.3) based on their grade point average (GPA). We also analyzed their error-related negativity (ERN), an electrophysiological measure that potentially reflects academic performance, during an arrowhead version of the flanker task to assess cognitive control of action monitoring. Participants with a low body mass index were found to have lower GPAs. Furthermore, the underweight students exhibited smaller ERN amplitudes, which indicates decreased cognitive control in action monitoring. These findings suggest that a healthy weight status is essential for effective cognitive functioning and academic success in young adult women, among whom being underweight is a serious health problem.