The purpose of this study was (a) to investigate gender differences in mental health among Danish youth soccer players, (b) to discover the mental health profiles of the players, and (c) to explore how career progression and mental health are related. A total of 239 Danish youth elite soccer players (M = 16.85, SD = 1.09) completed an online questionnaire assessing mental well-being, depression, anxiety, along with other background variables. Female players scored significantly lower on mental well-being and had four times higher odds of expressing symptoms of anxiety and depression than males. Athletes’ mental health profiles showed that most athletes experience low depression while having moderate mental well-being. Depression, anxiety, and stress scores generally increased when progressing in age, indicating that the junior–senior transition poses distinct challenges to players’ mental health, especially for female players. Different strategies to foster players’ mental health depending on their mental health profiles are proposed.