Empirical research regarding the prevalence of mental health symptoms in Paralympic athletes is scarce. We aimed to evaluate the prevalence of mental health concerns in elite Paralympic athletes based on their scores in the IOC Sport Mental Health Assessment Tool 1 (SMHAT-1) and the subsequent in-person clinical intake interviews. In doing so, we also compared the prevalence of mental health symptoms and recommendations in the cohorts of Paralympic and Olympic athletes. We administered the SMHAT-1 (a state-of-the-art tool comprising screeners of psychological distress, depressive and anxiety symptoms, sleep disturbances, alcohol and other substances misuse, and disordered eating) during the routine biannual medical check-ups for all Paralympic athletes at the National Centre for Sports Medicine in Poland. Subsequently, all Paralympic athletes were interviewed by qualified sport psychologists who further evaluated the athletes’ mental health and provided recommendations. A total of 137 Paralympic athletes (87 males, 50 females) participated in the study three to eight months prior to the 2024 Paris Paralympic Games; 61% scored above the triage threshold for psychological distress. Based on the subsequent mental health evaluation, 75.2% of Paralympic athletes required no mental health action, 18.3% were advised psychoeducation or sport psychologist consultation, while 7.3% were referred to a mental health specialist—a psychotherapist and/or a psychiatrist. The proportion of mental health recommendations did not significantly differ between Paralympic and Olympic athletes. The SMHAT-1 proved a valuable basis for the subsequent brief clinical interviews, substantially elevated the efficacy of mental health evaluation, and aided in raising mental health literacy in Paralympic athletes.