Anti-inflammatory agents such as long-chain n-3 fatty acids have been recognised to improve disease-related fatigue. We hypothesised that α-linolenic acid may also benefit in reduction of fatigue in low-grade inflammation such as overweight/obesity. Seventy-two healthy children and adolescents with BMI > 25 kg/m2 were randomised to flaxseed (n 38) and puffed wheat (n 34) groups. Participants consumed isoenergetic amounts of either 20 g/d flaxseed or 25 g/d puffed wheat for 4 weeks. Fatigue, mood feelings (depression, anxiety and stress), appetite, energy intake, weight, height and waist circumference were measured. Analysis was performed based on per-protocol and intention-to-treat (ITT) approaches. Consumption of flaxseed decreased mental fatigue and caused a significant between-group difference (P < 0·001). Although no significant change in physical and total score of fatigue was observed in either group, a significant between-group difference occurred due to a more remarkable change in these parameters in the flaxseed group. General fatigue, motivation, activity and mood feelings did not change significantly between groups. Flaxseed showed less benefit than puffed wheat on anthropometric measures as it caused a smaller increase in height (0·53 (sd 0·89) v. 1·09 (sd 0·87) cm, P = 0·03) and reduction in BMI (–0·25 (sd 0·63) v. −0·67 (sd 0·56) kg/m2, P = 0·01) than puffed wheat. Appetite and waist circumference decreased in both groups, but no significant difference was observed between groups. In ITT analysis, only alteration in mental fatigue was significant. In conclusion, consumption of flaxseed may improve mental fatigue in children with overweight/obesity. However, because of smaller increase in height, it is better to hinder administration of flaxseed during periods of growth.