BackgroundA mechanism-based approach to the evaluation and management of pain has been suggested across disciplines in contemporary research. However, the translation of pain mechanism assessment strategies in research to clinical practice is unclear. This study sought to explore perceptions and use of clinical pain mechanism assessment by physical therapists managing musculoskeletal pain.MethodsThis was an electronic cross-sectional survey. After initial development, refinement, and piloting for comprehensiveness, comprehensibility and relevance, the survey was disseminated to members of the Academy of Orthopaedic Physical Therapy via email listserv. Data was maintained anonymously using the online database REDCap. Descriptive statistics and Spearman’s correlations for non-parametric data were analyzed for frequencies and associations across variables.ResultsIn total, 148 respondents completed all aspects of the survey. Respondent age ranged from 26 to 73 years, with a mean (SD) of 43.9 (12.0). Most respondents (70.8%) reported performing clinical pain mechanism assessments at least ‘sometimes’. A majority (80.4%) believed clinical pain mechanism assessments are useful in guiding management strategies while 79.8% reported specifically choosing interventions to alter aberrant pain mechanisms. The most commonly used pain severity, physical examination testing and questionnaires were the numeric pain rating scale, pressure pain thresholds and pain diagrams, respectively. However, the vast majority of instruments to clinically assess pain mechanisms were performed by a small proportion of respondents (< 30%). There were no significant correlations between age, years of experience, highest earned degree, completion of advanced training or specialist certification and testing frequency.ConclusionThe evaluation of pain mechanisms involved in the pain experience is becoming common in research. The clinical application of pain mechanism assessment is unclear. Based on the results of this survey, physical therapists in the orthopedic setting believe pain mechanism assessment is useful, but data suggests it is infrequently performed. Additional research to uncover clinician motivation related to pain mechanism assessment is warranted.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12891-023-06618-0.