Background A growing line of research has sought to characterize the different presentations of autism spectrum disorder (ASD) among boys and girls. Much less is known about maternal experience and mother–child relationship in children with ASD based on child gender. The present qualitative study aimed to investigate the mother–daughter relationship from the perspective of mothers who are raising girls with ASD with normal intelligence and functional verbal communication. Methods Eleven in‐depth interviews were conducted with mothers of girls with ASD, ages 10–19 years. Data were analysed in an interactive process commonly used in naturalistic inquiry. Results provide insight into the unique maternal experience of raising a daughter with ASD. Results Mothers reported a sense of exclusion from the neurotypical population and male‐dominant ASD population and transformation in relationship. Themes identified were skepticism and delayed diagnosis, disbelief from others, lack of information about girls with ASD, higher social demands in adolescence, puberty challenges around hygiene, disappointment about physical appearance, vulnerability in relationships and worries about future functioning. The mother–daughter relationship started with an early expectation of a close and intimate relationship that then underwent a transformation, which challenged maternal competence, reshaped expectations and created a different bond between mother and daughter. Conclusions The findings in this qualitative study highlight the impact of gender on the maternal experience of raising a daughter with ASD and contribute to a better understanding of the needs of both mothers and daughters. These results can help providers support the mother–daughter dyad by recognizing gender‐specific challenges.