Objective To determine whether oral protein energy supplements, used long term in children with cystic fibrosis who are moderately malnourished, improve nutritional and other outcomes. Design Multicentre randomised controlled trial. Setting Seven specialist paediatric cystic fibrosis centres and their associated shared care clinics and seven smaller paediatric cystic fibrosis clinics. Participants 102 children with cystic fibrosis, aged between 2 and 15 years, who were moderately malnourished. Interventions Oral protein energy supplements in addition to usual dietary advice compared with dietary advice alone, for 12 months. Main outcome measure Change in body mass index centile over one year. Results Use of supplements was not associated with a change in body mass index centile (mean difference 2.99 centile points, 95% confidence interval − 2.70 to 8.68) or other nutritional and spirometric outcomes in this group of children. Conclusions Long term use of oral protein energy supplements did not result in an improvement in nutritional status or other clinical outcomes in children with cystic fibrosis who were moderately malnourished. Oral protein energy supplements should not be regarded as an essential part of the management of this group of children. Trial registration ISRCTN: 95744468.