The main purpose of the current study was to analyze the injury incidence, characteristics and burden among sub-elite female futsal players. Individual exposure to match play and training, injury incidence and characteristics (player position, injury mechanism, type of injuries, severity of injuries, recurrent vs. new injuries, season variation of injury pattern) in a female futsal team were prospectively recorded for three consecutive seasons (2015–2018). Incidences were calculated per 1,000 h of exposure. A total of 30 injuries were reported during the three seasons within a total exposure of 4,446.1 h. The overall, match and training incidence of injuries were 6.7, 6.4 and 6.8 injuries/1,000 h of exposure, respectively. Most injuries had a non-contact mechanism (93%), with the lower extremity being the most frequently injured anatomical region (5.62 injuries/1,000 h of exposure). The most common type of injury was muscle/tendon (4.9 injuries/1,000 h of exposure) followed by joint (non-bone) and ligament (1.3 injuries/1,000 h of exposure). The injuries with the highest injury burden were those that occurred at the knee (31.9 days loss/1,000 h exposure), followed by quadriceps (15.3 day loss/1,000 h) and hamstring (14.4 day loss/1,000 h) strains. The first few weeks of competition after pre-season and soon after the Christmas break were the time points when most injuries occurred. These data indicate that sub-elite female futsal players are exposed to a substantial risk of sustaining an injury. To reduce overall injury burden, efforts should be directed toward the design, implementation and assessment of preventative measures that target the most common diagnoses, namely, muscle/tendon and ligament injuries.