Autistic people are over-represented at gender clinics, but there is limited research to guide clinical practice with this group. We investigated the perspectives of clinicians working with autistic patients who experience gender dysphoria. We asked clinicians about the relationship between autism and gender dysphoria, and whether they work differently with this patient group. We recruited clinicians from young person and adult gender clinics and autism services (n = 16). We analysed the interview transcripts using interpretative phenomenological analysis (IPA). The first overarching theme was clinician understanding of the intertwined experiences of patients, with four subthemes: (a) coming to an individualised understanding of autism, gender dysphoria, and mental health; (b) different ways of thinking about gender; (c) social differences as barriers and facilitators to gender comfort; (d) the challenge of sensory sensitivities and puberty. The second overarching theme was mismatch of patient and clinician communication styles and goals, with three subthemes: (a) different communication of gender needs; (b) changing clinical sessions to overcome barriers; (c) tension between clinician and patient aims and thinking styles. We conclude that autism adaptations should be made in gender settings, by increasing clinician understanding of how autism and gender dysphoria can intersect, as well as by making adjustments to clinic processes.