Background Flourishing is a multi-dimensional construct that encompasses physical, psychological and social well-being. A proposed positive attribute of flourishing is resilience, which is the ability to bounce back despite the presence of stressors. A common stressor among athletes is overuse injuries, which may negatively affect well-being. Objective To examine the relationships of resilience and overuse injury with flourishing in collegiate athletes. Materials and methods 253 college athletes participated. The Flourishing Scale, Oslo Sports Trauma Research Center Overuse Injury Questionnaire (OSTRC), and Brief Resilience Scale (BRS) were administered via online questionnaire. For OSTRC scores, athletes were classified into injury and participation status groups. For BRS scores, athletes were classified into low resilience (LR), normal resilience (NR), and high resilience (HR) groups. Results Median flourishing score was 50.0 (46.5–53.5); mean BRS score was 21.6 (SD 4.3). Overuse injury and substantial overuse injury incidence proportion (IP) were 25.4 (95% CI: 20.3, 30.5) and 9.1 (95% CI: 7.0, 11.2). The IP for participants unable to play was 15.1 (95% CI: 12.9, 17.2). Significant differences were found in flourishing among resilience groups (p = 0.002) but not among overuse injury groups (p = 0.140) or participation variables (p = 0.205). Conclusion College athletes demonstrated high flourishing scores. Flourishing demonstrated a significant relationship with resilience across all groups but not among overuse injury or participation status. This finding indicates that college athlete well-being is strongly associated with resilience. Future longitudinal studies are needed to determine if resilience can be modified to positively influence athlete well-being.