This pilot randomized controlled trial (RCT) investigated benefits of omega-3 fatty acid supplementation and Individual-Family Psychoeducational Psychotherapy (PEP; a family-focused, cognitive-behavioral therapy) for behavior problems among youth with depression. Participants aged 7-14 with DSM-IV-TR depressive disorders (N = 72; 56.9 % male) were randomized to 1 of 4 treatment conditions: PEP + omega-3, PEP monotherapy (with pill placebo), omega-3 monotherapy, or placebo (without active intervention). At screen, baseline, and 2, 4, 6, 9, and 12 weeks post-baseline, parents completed the SNAP-IV, which assesses attention-deficit/hyperactivity disorder symptoms, oppositional defiant disorder symptoms, and overall behavior problems. At screen, baseline (randomization), 6 and 12 weeks, parents completed the Eyberg Child Behavior Inventory (ECBI), which includes Intensity and Problem scales for child behavior problems. Youth who had a completed SNAP-IV or ECBI for at least two assessments during treatment (n = 48 and 38, respectively) were included in analyses of the respective outcome. Linear mixed effects models indicated a significant effect of combined PEP + omega-3 on SNAP-IV Total (p = 0.022, d = 0.80) and Hyperactivity/Impulsivity trajectories (p = 0.008, d = 0.80), such that youth in the combined group saw greater behavioral improvement than those receiving only placebo. Similarly, youth in combined treatment had more favorable ECBI Intensity trajectories than youth who received no active treatment (p = 0.012, d = 1.07). Results from this pilot RCT suggest that combined PEP + omega-3 is a promising treatment for co-occurring behavior symptoms in youth with depression.