Background Peer relationships are an important indicator of adolescents’ school-based mental health and social adjustment, but experimental evidence on whether cognitively engaging physical activity (CEPA) improves them remains limited. This trial tested the effect of a CEPA curriculum on peer relationships relative to a traditional physical education curriculum (TPEC), with exploratory pathways through executive function and cognitive reappraisal. Methods In this parallel two-arm cluster randomized controlled trial, 12 intact classes comprising 650 students in grades 10 and 11 from three urban public high schools in eastern China were randomly assigned within school-by-grade strata to 12 weeks of CEPA or TPEC (three 45-min sessions per week; six classes per arm). The primary outcome was the posttest total peer relationship score; secondary outcomes were executive function and cognitive reappraisal. Analyses followed the intention-to-treat principle, using linear mixed models with class random intercepts and multiple imputation; serial mediation was examined in exploratory analyses with Monte Carlo confidence intervals. Results 650 students entered baseline assessment (CEPA, 327; TPEC, 323) and 612 (94.2%) completed the posttest. CEPA improved peer relationships relative to TPEC (between-group difference, 4.39 points; 95% CI, 0.64 to 8.13; d = 0.38; p = 0.029). Between-group differences for executive function (2.28; 95% CI, − 0.22 to 4.79; d = 0.35) and cognitive reappraisal (1.38; 95% CI, − 0.13 to 2.90; d = 0.36) were not statistically significant after Holm correction. Exploratory indirect-effect estimates through executive function, cognitive reappraisal, and their serial pathway were positive, with 95% confidence intervals that included zero. The primary result was consistent across sensitivity analyses, and observed contamination in TPEC classes was 2.3% of sessions. Conclusions A 12-week CEPA curriculum improved adolescents’ peer relationships relative to traditional physical education. Executive function and cognitive reappraisal remain candidate pathways for further testing. CEPA offers a practical approach within routine school physical education. Trial registration Chinese Clinical Trial Registry, ChiCTR2500114337 (retrospectively registered 10 December 2025).
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