Currently, there is little research investigating how schools can support the mental health and social development of young people with cystic fibrosis (CF), given their heightened risk of mental illness. Few studies have examined the relationship between bullying and mental health in populations of children with CF. This study describes the peer bullying experiences of young people with CF, and examines associations between school bullying and the psychological well-being of these young people. A sequential mixed-methods approach was used to collect data from 26 young people with CF (10−16 years of age). These data were compared with large samples of healthy children. Following an online survey, 11 young people, through online focus groups, expanded on the survey findings, describing their experiences within the school environment. Young people with CF reported lower involvement in bullying victimization and perpetration relative to the comparison population. For older adolescents with CF, victimization was associated with less connectedness to school and less peer support, and more school loneliness, anxiety, and depression. Young people with CF reported they generally liked the school environment, and were happy with their friendships, whereas some older adolescents reported that bullying evoked anxiety and mood problems. Reported bullying was primarily verbal and targeted characteristics of their CF, including their coughing, noninvolvement in certain activities because of shortness of breath, use of medication, and being underweight (for boys only). The findings provide some recommendations for interventions to promote mental health and school engagement among young people with CF.