The annual prevalence of musculoskeletal disorders among participants was 158 (48.5%) with [95% CI: 43%, 54%], opportunistic infection [AOR, 10.43; 95% CI = 2.76–42.25], type of ART medication used, CD4-count [AOR, 0.13; 95% CI 0.03–0.85], and change in anti-retroviral therapy regimen change [AOR, 8.14; 95%CI 2.06–32.09] were significantly associated with musculoskeletal disorders. Here, CD4 is linked to musculoskeletal system disorder.