Badminton is a popular sport with a rich tradition in Pakistan twin cities Islamabad and Rawalpindi. In badminton, players are more susceptible to certain musculoskeletal problems due to the sport's dynamic character, abrupt accelerations and decelerations. Badminton has an injury rate of 1 to 7/1000 hours per person of playing time. Objective: To find out prevalence of musculoskeletal problem including pain among the badminton players played in various clubs of Islamabad and Rawalpindi. Methods: 255 badminton players participated in a convenience sample-based cross-sectional study after ethical permission. The incidence of musculoskeletal discomfort in novice badminton players' shoulder, elbow, wrist, hands, thigh, hips, knee and ankle was measured using a self-drafted survey and the Nordic Musculoskeletal Questionnaire. Data collection was done sports clubs of Islamabad and Rawalpindi. Study ran from September 22, 2021, to June 30, 2022. SPSS version-25 software was used for data analysis. Results: The results showed prevalence was 16.5, back 18.4, hip 7.4, knee 28.6, ankle 16.5, elbow 22.4, wrist 21.2, low back 12.9, and shoulder 49.4. Among badminton players, the most common pain regions were the shoulder and knee. Other areas that players are less likely to have discomfort in include the hands, hips and ankles. Conclusions: Conclusions of study showed younger athletes had higher prevalence of musculoskeletal discomfort. Most prevalent pain areas among badminton players were the knee and shoulder.