The aim of this study was to investigate the incidence of back pain in young basketball and floorball players under 21 years of age. The secondary aim was to examine risk factors especially for low back pain (LBP). Nine basketball and nine floorball teams (n = 396) participated in this prospective follow‐up study (2011‐2014). Young athletes (mean age 15.8 ± 1.9) performed physical tests and completed a questionnaire at baseline. The follow‐up lasted 1‐3 years per player. During the follow‐up, back pain reported by the players was registered on a weekly basis and verified by a study physician. The exposure time (AE) on team practices and games was recorded by the coach. Altogether back pain was reported 61 times by 51 players. The incidence of back pain was 87 per 1000 athlete‐years and 0.4 per 1000 hours of AE. Hamstrings, quadriceps and iliopsoas extensibility and general joint hypermobility were not associated with LBP. Furthermore, no association between LBP and leg extension strength or isometric hip abduction strength asymmetry was found in these young basketball and floorball players. In conclusion, back pain can lead to a considerable time‐loss from training and competition among young basketball and floorball players and the pain tends to reoccur. Lower extremity muscle extensibility, general joint hypermobility or investigated lower extremity strength measures were not associated with the risk of LBP.