Unlike musculoskeletal (MSK) injuries, MSK pain is rarely studied in athletes. In this study, we examined the prevalence of preseason MSK pain in apparently healthy collegiate soccer and basketball players and its relationship with previous injuries (1-year history), among other factors. Ninety-seven eligible student athletes (mean age: 20.1 (SD: 1.6) years; 43% male; 53% soccer players) completed a baseline questionnaire comprising questions related to demographics, medical and 1-year injury history and any current MSK pain and the corresponding body location. The overall prevalence of preseason MSK pain was 26% (95% CI: 17–36%) and it did not differ by sex or sport. The back (6.2%) and knee (5.2%) regions were reported to be the most frequently affected body parts for preseason MSK pain. Athletes with a previous injury and with perception of incomplete healing had 3.5-fold higher odds (OR: 3.50; 95% CI: 1.28–9.36) of baseline MSK pain compared with those without a previous injury. One in four collegiate soccer and basketball players had preseason MSK pain. Collegiate sports medicine professionals should consider conducting routine preseason evaluations of MSK pain in their athletes and initiate appropriate interventions for the prevention of MSK pain and its potential consequences among athletes.