Abstract Public transport systems continue to gain ground as a cornerstone of sustainable urban mobility, offering alternatives to private car use, city congestion, and pollution. In this context, the shift toward regular public transport use seems influenced by several factors, with previous studies suggesting that safety concerns, service quality, and environmental value are key predictors of public transport usage intention. However, gender-based differences in travelers’ intentions and choices remain underexplored. Aim This research aimed to investigate gender differences in public transport usage intentions, focusing on the role of individual, psychosocial, and transport system-related factors as structural predictors. Methods This study used data from 820 Spanish public transport travelers, evenly divided by gender. The data, collected through an electronic survey, were analyzed using Multi-Group Structural Equation Modeling (MGSEM) to assess gender-based differences in the relationships between literature-based predictors and public transport usage intentions. Results The multivariate analyses showed significant gender differences in the perception of public transport system features and usage intentions. While both genders reported high concerns regarding security threats, women placed greater emphasis on sustainability contributions in their transport choices. Moreover, although extrinsic incentives did not significantly predict usage intentions, sustainability dissemination did so for both genders, suggesting that effective communication may help overcome the lack of influence from such incentives in promoting public transport usage intentions. Conclusion The findings of this study highlight gender-sensitive differences regarding specific concerns related to safety, service quality, inclusiveness, and the sustainability value of public transport, beyond the differential influence of these factors on ridership levels. Policy implications These outcomes support the need to address gender-specific needs that could enhance the effectiveness of public transport systems and support broader sustainable mobility goals.