Abstract Background Previous studies reported that poor sleep quality (PSQ) was associated with musculoskeletal pains (MSP) and poor physical performance in athletes. Objective The current study aimed at determining PSQ and its associations with MSP in some sub-Saharan athletes. Methods A cross sectional study was conducted among 205 highly trained and 115 elite athletes (aged: 25 ± 2 years, Body mass index: 22.8 ± 0.9 kg/m²) in Dakar, Senegal, during a competitive season in a variety of sport disciplines including athletics, basketball, football, rugby, wrestling, tennis. Quality of sleep and MSP were assessed using the French version Pittsburgh Sleep Quality Index (PSQI) and French version of Nordic questionnaire respectively. Pain on body joints during a week was defined as seven-day MSP (MSP-7d) and PSQ for a PSQI > 5. Results 27.8% (95%CI: 23.2–32.9) of the overall sample suffered PSQ, with 33.7% (95%CI: 24.7–44.0) in basketball and 24.7% (95%CI: 16.9–34.6) in football. According to athletic status and gender, PSQ was more prevalent among highly trained (66.3; 95%CI: 55.9–75.3) and men (69.7%; 95%CI: 59.5–78.7). Among athletes with PSQ 43.8% (95%CI: 33.9–54.2) suffered MSP-7d, with 36.6%; highly trained (95%CI: 23.7–42.9) and 28.1% female. Considering body region, hips/thigh (14.6%; 95% CI: 8.74–23.4) and upper back (13.5%; 95%CI: 7.88 -21, 1) were more affected. Basketball players were more affected from MSP (MSP-7d = 38.5%; 95%CI: 24. 9–54.1) on high on wrists/hands (MSP-7d = 44.4%; 95%CI: 18.9 -73.3; P = 0.04). Based on athletic status, MSP-7d were higher on highly trained necks (100%; 95%CI: 56.1–100; p = 0.04). PSQ was associated with basketball (OR: 3.062, 95%CI: 1.130–8.300, p = 0.02) compared to Athletic. PSQ and MSP-7d were associated on Wrist/hands (OR: 3.352, 95%CI: 1.235–9.099, p = 0.01), and at the upper back (OR: 5.820, 95%CI: 2.096–16.161, p = 0.0007). Conclusion These results indicate that PSQ is considerable among Senegalese athletes and is associated with MSP during a week. Hence, we recommend to look for strategies optimizing good quality of sleep in order to reduce pains, to improve health.