This longitudinal study explored family functioning and relationship quality for adolescents with severe anorexia nervosa (AN). An important outcome given healthy family functioning supports effective adolescent development. Fifty‐four female adolescents and their parents, treated with family‐based treatment after inpatient admission, and 49 non‐clinical age‐matched adolescents and their parents were compared at assessment and 6 months after session 20. At baseline, AN group mothers and fathers reported poorer family function. AN adolescents were notably similar to controls, reporting poorer function in only one domain. There were no changes for adolescents, an improvement for mothers in the AN group, but an increase in perceived impairment for fathers in both groups, with AN fathers more affected. The similarity in adolescent reports and the increase for fathers over time may indicate that normal adolescent family processes occur even in the midst of serious illness. There is a need to provide intervention to ameliorate the impact of treatment on parents. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association.