BACKGROUND: Improvements in executive functioning (EF) may lead to improved quality of life and lessened functional impairment for children with mood disorders. The aim was to assess the impact of omega-3 supplementation (Omega3) and psychoeducational psychotherapy (PEP), each alone and in combination, on EF in youth with mood disorders. We completed secondary analyses of two randomized controlled trials (RCTs) of Omega3 and PEP for children with depression and bipolar disorder. METHODS: Ninety-five youths with depression or bipolar disorder not otherwise specified/cyclothymic disorder were randomized in 12-week RCTs. Two capsules (Omega3 or placebo) were given twice daily (1.87 g Omega3 total daily, mostly eicosapentaenoic acid). Families randomized to PEP participated in twice-weekly 50-min sessions. Analyses assess impact of interventions on the Behavior Rating Inventory of Executive Functioning (BRIEF) parent-report Global Executive Composite (GEC) and two subscales, Behavior Regulation (BRI) and Metacognition (MI) Indices. Intent-to-treat repeated measures ANOVAs, using multiple imputation for missing data, included all 95 randomized participants. Trials were registered with www.clinicaltrials.gov, NCT01341925 & NCT01507753. RESULTS: Participants receiving Omega3 (aggregating combined and monotherapy) improved significantly more than aggregated placebo on GEC (p = .001, d = .70), BRI (p = .004, d = .49), and MI (p = .04, d = .41). Omega3 alone (d = .49) and combined with PEP (d = .67) each surpassed placebo on GEC. Moderation by attention-deficit/hyperactivity disorder (ADHD) comorbidity was nonsignificant although those with ADHD showed nominally greater gains. PEP monotherapy had negligible effect. CONCLUSIONS: Decreased impairment in EF was associated with Omega3 supplementation in youth with mood disorders. Research examining causal associations of Omega3, EF, and mood symptoms is warranted.