Background and objectives: Handball is a popular sport among women whose practice can lead to marked health benefits but could also show a high injury risk. There is a lack of research on intermediate level female players. We aimed to identify the prevalence of sport injuries in amateur and young intermediate level female handball players and the potential influence of the sport category. Materials and Methods: A group of cadets, juvenile and senior female players of three handball clubs participating in the Spanish regional league were followed throughout the 2018–2019 season. Information on injuries and exposure was collected via questionnaires. Results: Out of 114 players (34 seniors, 33 juvenile and 47 cadets), 77 of them sustained at least one injury. Most of the injuries were either moderate or severe, regardless of the category. A total of 7.93, 5.93 and 4.16 injuries per 1000 h of exposure were registered in the senior, juvenile and cadet categories respectively. The risk of sustaining an injury was 2.14 times higher for senior players Confidence Interval (CI 95%: 1.51–3.03) and 1.92 higher for juvenile players (CI 95%: 1.32–2.78) when compared with cadets. Conclusions: Senior and young female handball athletes playing at an amateur and intermediate level, are exposed to a substantial risk of sustaining a moderate or severe injury. The players’ category does not seem to have a great impact on the injury rate and on the characteristics of the sport injuries registered.