OBJECTIVE: To examine the associations between career choice motivation and professionalism among medical students based on gender in the context of COVID-19. DESIGN: Cross-sectional study. SETTING: The study was conducted at a medical school in China. METHODS: A total of 1421 second-year to fourth-year medical students participated in the survey using cluster sampling. They were asked to complete questionnaires on demographic information, career choice motivation and professionalism. Linear regression models were used to analyse the relationship between career choice motivations and professionalism based on gender differences. RESULTS: Female medical students outperformed males in professionalism (p<0.001). Third-year medical students have the lowest level of professionalism irrespective of gender. In addition, females have more intrinsic career choice motivation than males. Students motivated by had the highest level of professionalism, while those who had the lowest. According to the linear regression analysis, the motivation was the factor of professionalism in male medical students (p<0.05). However, the motivation negatively influenced the professionalism of female medical students (p<0.05). CONCLUSION: The level of professionalism differed between genders based on different career choice motivations. Career choice motivation can be used as an entry point for professionalism education among medical students. Targeted interventions should be implemented to improve professionalism, especially for male medical students and unmotivated students.