Purpose The aim of the study was to explore and explain two hypothesized indirect longitudinal pathways and investigate gender differences in linking parenting factors to adolescents' sexual emotions. The general pathway expected higher parent–adolescent relationship quality to be related to more positive and less negative sexual emotions through higher adolescent global self-esteem. The sexuality-specific pathway expected more frequent parent–adolescent sexual communication to be related to more positive and less negative sexual emotions through higher adolescent sexual autonomy. Methods Online questionnaire data were used from three waves of Project STARS, a longitudinal study on adolescent sexual development. The analysis sample included 248 sexually experienced adolescents (M = 14.74 years at baseline). Adolescents reported on the quality of their parent–adolescent relationship, how often they discussed sexual topics with their parents, their global self-esteem, sexual autonomy, and experience of positive (happy, proud, and loved) and negative (dirty, ashamed, and guilty) emotions after having sex. Results Overall, adolescents experienced more positive than negative emotions after sex. Mplus path model results indicated that, first, higher parent–adolescent relationship quality was related to higher adolescent global self-esteem, but global self-esteem was not related to sexual emotions. Second, more frequent parent–adolescent sexual communication was related to more adolescent sexual autonomy, and more sexual autonomy was related to more positive and less negative sexual emotions. However, no significant indirect effects, nor gender differences were found. Conclusions Adolescents' sexual autonomy appears to play a particularly important role in how they experience having sex. Concrete suggestions for how the development of adolescents' sexual autonomy may be supported are discussed.