In athletes, injuries and medical conditions affecting the upper extremities are quite common. However, there has been limited research on the occurrence of joint pain in the peripheral upper extremities among elite athletes. Thus, this study aimed to determine how prevalent upper limb pain and disability are among team sports players, particularly in football, ice hockey and floorball. We also aimed to compare the severity of pain and disability among these sports and assess the risk of developing upper limb pain in athletes. This cross-sectional study was conducted between June 2021 and September 2022, involving 388 male elite athletes from national-level sports clubs. The prevalence of shoulder pain and disability was determined using the Shoulder Pain and Disability Index (SPI). Assessment of elbow pain and disability was conducted using the Oxford Elbow Score (OES), while wrist pain and disability were evaluated through the Patient-Rated Wrist Evaluation (PRWE). Significant differences in total SPI, OES and PRWE scores were observed among all groups. Ice hockey players experienced the highest levels of shoulder and wrist pain. Compared to football and floorball players, ice-hockey players had a 2.13 times higher risk of shoulder pain, with a pain incidence of 40.8%. Ice hockey also had a 1.71 times higher risk of wrist pain than football, with a pain prevalence of 26.3%. Notably, floorball players exhibited the most pronounced elbow pain, with a 13.18-fold higher risk than football and ice-hockey players and a pain prevalence of 67.2%. The study findings suggest that ice hockey players experience the highest pain levels in their right limbs, whereas football players have the lowest pain levels, underscoring the importance of dedicating more attention to developing innovative, effective and advanced preventive programs for athletes.