Background: Malnutrition has extensive consequences, affecting multiple levels of functioning, including motor skill impairments. However, current interventions have mainly focused on dietary treatment, often neglecting motor impairments and relying solely on clinical and anthropometric indicators to assess treatment response. This study aims to bridge this gap by examining the combined effect of ready-to-use supplementary food (RUSF) and high-intensity motor learning (HiML) on motor skill-related physical fitness in children with moderate thinness (MT). Methods: A cluster randomized controlled trial was conducted among children 5–7 years old with MT in Jimma Town. Three schools were randomized to three intervention arms, including a total of 69 children: RUSF (n = 23), RUSF + HiML (n = 25), and no intervention (n = 21). The HiML training was applied for 12 weeks, and RUSF was distributed daily for 12 weeks. HiML was given daily (1 h/day, 5 days/week). The primary outcome was motor skill-related physical fitness assessed at baseline and endline using the performance and fitness test battery (PERF-FIT). The changes from baseline to endline measurements were calculated as differences, and the mean difference in these changes/differences (DID) was then computed as the outcome measure. AN(C)OVA was used to directly investigate differences between groups. Statistical significance was declared at p-value ≤ 0.05. Results: There was a significantly greater and comparable improvement in both the RUSF and RUSF + HiML groups compared to the control group for the ‘stepping’ item (p < 0.001), the ‘side jump’ item (p < 0.001), the ‘standing long jump’ (p < 0.001) and the ‘jumping and hopping’ total (p = 0.005). The RUSF + HiML group showed significantly greater improvements in the ‘bounce and catch’ (p = 0.001) and ‘throw and catch’ (p < 0.001) items compared to the RUSF group, which, in turn, demonstrated greater improvement than the control group in both items (p < 0.01). Conclusions: A 12-week combination of RUSF + HiML was proven to be safe in children with MT and caused clear improvements in motor skill-related physical fitness. When the children received RUSF with HiML training, similar gains in stepping, side jump, standing long jump, and jumping and hopping were observed, except for the ball skills where the HiML training group performed better.