Cambodia continues to have a high prevalence of acute malnutrition. Low acceptability has been found for standard ready-to-use-therapeutic-food (RUTF) products. Therefore, NumTrey, a locally-produced fish-based RUTF, was developed. The objective was to evaluate the effectiveness of NumTrey compared to an imported milk-based RUTF for weight gain among children aged 6–59 months in the home-treatment for acute malnutrition. Effectiveness was tested in a single-blinded randomized controlled trial with weight gain as the primary outcome. Anthropometry was assessed at baseline and bi-weekly follow-ups until endline at Week 8. In total, 121 patients were randomized into BP-100TM (n = 61) or NumTrey (n = 60). There was no statistical difference in mean weight gain between the groups (1.06 g/kg/day; 95% CI (0.72, 1.41) and 1.08 g/kg/day; 95% CI (0.75, 1.41) for BP-100™ and NumTrey, respectively). In addition, no statistically significant differences in secondary outcomes were found. Although the ability to draw conclusions was limited by lower weight gain than the desired 4 g/kg/day in both groups, no superiority was found for eitherRUTF. A locally produced RUTF is highly relevant to improve nutrition interventions in Cambodia. A locally produced fish-based RUTF is a relevant alternative to imported milk-based RUTF for the treatment of SAM in Cambodia.