This mixed-methods study examined gender differences in the friendships and conflict experiences of autistic girls and boys relative to their neurotypical peers. In total, 102 adolescents (27 autistic girls, 26 autistic boys, 26 neurotypical girls, and 23 neurotypical boys), aged between 11 and 18 years completed the Friendship Qualities Scale, the Revised Peer Experiences Questionnaire and were interviewed about their friendships. Results demonstrated that in many ways, the friendships and social experiences of autistic girls are similar to those of neurotypical girls. Autistic girls, however, have significantly more social challenges than their neurotypical peers, experiencing more conflict and finding that conflict harder to manage successfully. Autistic boys showed quantitatively different friendship patterns to all other groups. There were consistent gender differences in the type of conflict which boys and girls experienced, regardless of diagnostic status. These findings suggest that gender, rather than diagnosis per se, plays a critical role in the way that autistic adolescents perceive and experience their social relationships.