The purpose of this study was to investigate the prevalence of self-reported restrictive eating, current or past eating disorder, and menstrual dysfunction and their relationships with injuries. Furthermore, we aimed to compare these prevalences and associations between younger (aged 15–24) and older (aged 25–45) athletes, between elite and non-elite athletes, and between athletes competing in lean and non-lean sports. Data were collected using a web-based questionnaire. Participants were 846 female athletes representing 67 different sports. Results showed that 25%, 18%, and 32% of the athletes reported restrictive eating, eating disorders, and menstrual dysfunction, respectively. Higher rates of lean sport athletes compared with non-lean sport athletes reported these symptoms, while no differences were found between elite and non-elite athletes. Younger athletes reported higher rates of menstrual dysfunction and lower lifetime prevalence of eating disorders. Both restrictive eating (OR 1.41, 95% CI 1.02–1.94) and eating disorders (OR 1.89, 95% CI 1.31–2.73) were associated with injuries, while menstrual dysfunction was associated with more missed participation days compared with a regular menstrual cycle (OR 1.79, 95% CI 1.05–3.07). Our findings indicate that eating disorder symptoms and menstrual dysfunction are common problems in athletes that should be managed properly as they are linked to injuries and missed training/competition days.