Stigma is an important contributor to social isolation and has negative wellbeing and health impacts. People with intersex variations experience stigma based on multiple factors – family-based silencing and stigma; lack of adequate puberty education normalising body diversity at school; and medically imposed stigma from ‘corrective’ interventions. This article outlines theory concerning sex-based relational socialisation in schools for friendships and other relationships. It explores the literature on social isolation and exclusion and on students with intersex variations. It reports on the sex-based relational learning informed by the schooling experiences of 86 people with intersex variations aged 22–71 years, recruited from diverse international contexts. Students with intersex variations desired friendships with students of a different assigned sex more frequently than did endosex students. They had different friendship and dating patterns and greater experience of social isolation compared to endosex students in both primary/elementary and high/secondary school contexts. Almost all participants found surgical intervention to be inappropriate and the inappropriateness of the gender in which they are brought up was a strong predictor of negative sex-based relational learning experiences and social isolation. Data provide important arguments for young people with intersex variations to have greater bodily, sex and gender determining autonomy in school and related settings.