OBJECTIVE: Examine injury-related psychological distress and association with perceived running ability in injured runners. DESIGN: Prospective longitudinal study. PARTICIPANTS: Forty-three patients with a running-related injury. MAIN OUTCOME MEASURES: Data collection at initial physical therapy visit and 12-16 weeks later included Optimal Screening for Prediction of Referral and Outcome - Yellow Flag (OSPRO-YF) and Athlete Fear Avoidance Questionnaire (AFAQ) for injury-related psychological distress, and University of Wisconsin Running and Recovery Index (UWRI) for perceived running ability. OSPRO-YF composite score, total yellow flags, and yellow flags in each domain (negative mood, fear-avoidance, positive affect/coping) were calculated. RESULTS: UWRI score and OSPRO-YF composite score and yellow flags significantly improved over time, while AFAQ score and yellow flags in OSPRO-YF negative mood domain did not. AFAQ scores were significantly correlated with UWRI score at baseline, follow-up and change over time, while OSPRO-YF composite score and yellow flags were not. Baseline OSPRO-YF composite score and AFAQ score were not correlated with follow-up UWRI score. CONCLUSIONS: Injury-related psychological distress is elevated when injured runners start rehabilitation, and generally improves; however, negative mood and athletic fear-avoidance may persist. Higher athletic fear-avoidance is associated with lower perceived running ability at the same time point or interval.