Background and purpose: Clinical monitoring for the recovery of sports injuries is fundamental for a safe return to the sport. The identification of the psychometric properties of self-report functional questionnaires, which have been validated in the athlete population, may facilitate the appropriate selection of objective methodologies to assess the functional recovery of individuals with sport-related injuries. The aim of this study was to systematically review the literature on the psychometric properties of self-administered questionnaires that measure functionality in athletes with musculoskeletal conditions of the lower limb. Materials and methods: A comprehensive search was carried out in MEDLINE/PubMed, SPORTDiscus, Scielo, and Google Scholar databases up to 30 October 2019. Psychometric properties studies of self-reported questionnaires measuring functionality in sports population were included. The methodological quality was evaluated using the COSMIN methodology. Results: A total of 37 studies and 13 different questionnaires were included. Cross-cultural validity was the least reported psychometric property. Content validity was poorly reported in the majority of questionnaires. According to the COSMIN standards, LEFS, CAIT, HAGOS, ACL-RSI, VISA-P, and UWRI are valid and reliable questionnaires to determine patient-reported outcome measurements during the rehabilitation process of an athlete. Conclusion: The selection of the most appropriate questionnaire to assess functionality in athletes should consider: (1) the condition in which it has been validated, (2) the type of sport included, and (3) the quality of the psychometric properties of the available questionnaires.