The present study examined gender identity differences in student-athletes' mental health during the COVID-19 pandemic. Self-identified female (n = 47; 18-24 years) and male (n = 50; 18-26 years) student-athletes from a mid-sized U-sport Canadian university participated in an online survey assessing athletic identity (Academic and Athletic Identity Scale), mental toughness (10-item Mental Toughness Questionnaire), resilience (Brief Resilience Scale), anxiety (Generalized Anxiety Disorder Questionnaire), depressive symptoms (Patient Health Questionnaire depression module), and coping (Brief COPE). Results from one-way MANOVAs and follow-up ANOVAs revealed that women reported significantly lower resilience, worse anxiety, worse depressive symptoms, employed more emotional and instrumental coping strategies, and endorsed more self-blame compared to men; there were no gender identity differences in athletic identity or mental toughness. Gender-specific multivariate linear regressions highlighted that lower mental toughness was significantly related to heightened anxiety in men, whereas lower resilience was significantly related to heightened anxiety in women. Finally, lower mental toughness, but not resilience, was significantly associated with increased depressive symptoms for both women and men. Taken together, the present results encourage high-performance personnel to foster mental toughness and resilience in student-athletes—with distinct efforts to bolster resilience in student-athletes identifying as women—as these constructs may attenuate negative mental health consequences (i.e., elevated anxiety and depressive symptoms) of the COVID-19 pandemic.