Background: In Ethiopia, moderate thinness (MT) is a persistent issue among children. Yet, evidence on the effects of dietary supplementation and motor skills training in these children is limited. Objective: This study aimed to assess the effect of Ready-to-Use Supplementary Food (RUSF), whether or not combined with high-intensity motor learning (HiML), on weight, height, body composition, and muscle strength in children 5–7 years old with MT living in Jimma Town, Ethiopia. Methods: A cluster-randomized controlled trial was carried out among 69 children (aged 5–7) with MT assigned to receive RUSF (n = 23), RUSF + HiML (n = 25), or no intervention (control group, n = 21). A multivariable Generalized Estimating Equations model was used and the level of significance was set at alpha < 0.05. Results:At baseline, there were no significant differences in the outcome measurements between the RUSF, RUSF + HiML, and control groups. However, after 12 weeks of intervention, there were significant mean differences in differences (DIDs) between the RUSF group and the control arm, with DIDs of 1.50 kg for weight (p < 0.001), 20.63 newton (N) for elbow flexor (p < 0.001), 11.00 N for quadriceps (p = 0.023), 18.95 N for gastrocnemius sup flexor of the leg (p < 0.001), and 1.03 kg for fat-free mass (p = 0.022). Similarly, the mean difference in differences was higher in the RUSF + HiML group by 1.62 kg for weight (p < 0.001), 2.80 kg for grip strength (p < 0.001), 15.93 for elbow flexor (p < 0.001), 16.73 for quadriceps (p < 0.001), 9.75 for gastrocnemius sup flexor of the leg (p = 0.005), and 2.20 kg for fat-free mass (p < 0.001) compared the control arm. Conclusion: RUSF alone was effective, but combining it with HiML had a synergistic effect. Compared to the control group, the RUSF and RUSF + HiML interventions improved the body composition, height, weight, and muscle strength of the studied moderately thin children. The findings of this study suggest the potential that treating moderately thin children with RUSF and combining it with HiML has for reducing the negative effects of malnutrition in Ethiopia. Future research should explore these interventions in a larger community-based study. This trial has been registered at the Pan African Clinical Trials Registry (PACTR) under trial number PACTR202305718679999.