Background: Work-related musculoskeletal disorders (WRMSDs) are prevalent among healthcare professionals, significantly affecting physical therapists due to their hands-on treatment techniques. These disorders, particularly involving the thumb, result from repetitive stress and poor ergonomics, leading to chronic pain and functional impairment. Despite extensive research on WRMSDs in other body regions, the specific prevalence of thumb pain among physical therapists in Pakistan remains underexplored. This study aims to investigate the prevalence and contributing factors of work-related thumb pain among clinical physical therapists in Rawalpindi and Islamabad, addressing a critical gap in the current understanding of occupational health challenges faced by these professionals. Objective: The study was conducted to find out prevalence of work-related thumb pain among clinical physiotherapists of Rawalpindi & Islamabad. Methods: A descriptive cross-sectional study was conducted from September 2022 to February 2023 in Rawalpindi and Islamabad. Data was collected from 270 physiotherapists using self-structured questionnaire. Sample size was calculated using Slovin’s formula with confidence interval 95% and keeping margin of error 0.05%. Non-probability convenient sampling technique was used for collection of data. Data was analyzed by using SPSS version 26. Results: Out of 270 participants, 130 complained of thumb pain whereas 140 had no pain. The overall mean age of sample was 28.15±5.39. Among males 52(43.3%) had thumb pain and 68(56.7%) had no thumb pain. Females 78(52.0%) had thumb pain and 72(48.0%) had no thumb pain. 218(80.7%) participants were working from 1-5 years, 62(23%) worked for less than 15 hours per week, 84(31.1%) worked for 5 hours per day, 108(40%) treated up to 5 patients per day. Moderate intensity pain was present in 82(30.4%) participants. Mostly 67(24.8) were affected with MP joint pain site. Conclusion: Thumb pain was prevalent among clinical physiotherapists. Females were having more thumb pain as compared to male participants. The intensity of pain prevalent was moderate on NPRS. This thumb pain is due to their professional techniques including manual therapy, ischemic pressure release and massage. Most of the participants reported thumb pain due to mobilization and manipulation techniques.