In most societies, women are less likely to choose a science, technology, engineering and mathematics (STEM)-related study program than men. This problem persists despite numerous initiatives aimed at fostering the uptake of STEM subjects by women, who represent an underutilized source of talent in a time of great need for STEM professionals. Many reasons for women’s avoidance of the path into STEM-related areas have been discussed, including weaker mathematical skills, implicit gender stereotypes or structural deficits in school education. One variable which is presumably at the core of decisions regarding a specific study subject is motivation. We aim to look in greater depth at the basis for motivation by referring to self-determination theory (SDT). Here, we specifically focus on the needs for competence and autonomy which represent pivotal sources of motivation, effective performance and psychological well-being and are assumed to be positively correlated with academic achievement and perseverance. In line with previous SDT research, we assume that self-perceptions during STEM studies contribute to experiences of competence and autonomy and may be responsible for gender disparities. To examine whether and how a sex-specific perception of autonomy and competence influences decisions regarding STEM subjects, we conducted a survey study of Master’s students (N = 888; 461 female, 427 male), who were enrolled either in STEM or non-STEM subjects, and asked about students’ motivations, perceived competence (e.g., self-efficacy) and autonomy (e.g., volitional decision for a study major). The results revealed several main effects of study major and only a small number of interaction effects of sex and subject. For example, non-STEM students were more likely to enroll due to their stronger interest in their subject, signifying higher autonomy, while STEM students were more likely to select their subject according to their families’ wishes. The comparison between female and male STEM students revealed that males perceived more self-efficacy and reported more leadership aspirations while female STEM students have lower perceptions of their own competence, especially regarding perceived future competences.