This study aimed to explore the psychological perception of kinesiophobia and its impact on recovery barriers among injured athletes with chronic musculoskeletal conditions. A total of 65 athletes (50 males and 15 females) from Kerala, ranging from intercollegiate to national competitive levels, participated in the study. Inclusion criteria required participants to be aged 18–30, have experienced a musculoskeletal injury lasting more than three months, and have prior competitive sports experience. To assess the psychological impact of injury, six standardized tools were used: Tampa Scale of Kinesiophobia (TSK-17), Fear Avoidance Belief Questionnaire (FABQ), Pain Anxiety Symptom Scale (PASS), Injury-Psychological Readiness to Return to Sport (I-PRRS), WHO-5 Well-being Index, and Brief COPE Inventory. Data were collected both in-person and online and analyzed using SPSS.  Descriptive statistics, Independent t-tests, Mann-Whitney U tests, and normality tests were conducted. Findings revealed that a significant portion of athletes experienced high levels of kinesiophobia and ongoing fear of re-injury despite completing physical rehabilitation. Gender differences in psychological responses were minimal, though males showed significantly higher FABQ scores (p = 0.043). Athletes with higher kinesiophobia reported lower well-being scores (p = 0.001) and higher fear levels (p = 0.024), confirming the psychological burden associated with injury. The study concludes that psychological factors, especially kinesiophobia, play a critical role in athletes’ recovery and overall well-being. Despite limited psychological intervention in rehabilitation programs, many athletes expressed willingness to receive mental health support. These findings highlight the importance of integrating psychological assessment and intervention into sports injury rehabilitation to promote holistic recovery..