The aim of this study was to analyze the injury incidence in young trail runners according to the body region, type, mode of onset, and moment of occurrence, both in total and detailed by sex. Thirty-five male and sixteen female young elite trail runners, aged between 15 and 22 years, completed a questionnaire regarding the injury incidence in the last 2 years. Comparison of the proportions of the injury incidence within groups (all, male, and female runners) and between groups (male vs. female runners) was computed using z and Fisher’s exact tests. Results showed that most of the injuries in male runners occurred in ankle (54.3%; p < 0.001; ES = 0.520). New injuries were the most common type in male (60.0%; p < 0.001; ES = 0.829) and female runners (52.0%; p = 0.005; ES = 0.585). Acute sudden onset (55.7%; p = 0.002; ES = 0.722) and repetitive sudden onset injuries (48.0%; p = 0.002; ES = 0.141) were the most frequent in male and female athletes, respectively. Joint sprains (48.6%; p < 0.001; 0.464) were the most reported injuries in male runners. Comparative analysis between sexes showed that exacerbation injuries were higher in females (24.0%) than in male runners (8.6%), with p = 0.046 (ES = 0.205). However, female runners reported less incidence by acute sudden onset injuries (32.0%) than male runners (55.7%), with p = 0.042 (ES = 0.209). Young trail runners showed a specific injury profile due to the distinctive characteristics of the mountain terrain compared to the athletic modalities.