Ready-to-use therapeutic foods (RUTFs) are widely used to treat severe acute malnutrition (SAM) by improving key anthropometric outcomes; however, optimisation of RUTF formulations remains important to support sustained recovery. Rice bran, a novel nutrient-dense, prebiotic food ingredient, can support healthy growth. This two-arm, double-blinded, randomised controlled trial, compared the effectiveness of a locally produced RUTF with rice bran to the same RUTF without rice bran for the treatment of uncomplicated acute malnutrition in Jember, Indonesia. 200 children aged 6–59 months with SAM (WHZ < −3.0 and/or mid-upper arm circumference (MUAC) < 115 mm or having bilateral pitting oedema +/++) or approaching SAM (WHZ < −2.5) were enrolled in the study. Primary outcomes were weight, MUAC, and anthropometric z-scores. Linear mixed models were applied across all ages, and split by age groups (6–23 months and 24–59 months) at weeks 0, 4, 8, 12, and 16 for intention-to-treat (ITT) and per protocol analysis (PP). Children in two age groups were expected to respond differently to treatment based on their microbiome maturity. At week 4, the PP analysis revealed RUTF+rice bran treatment had significantly greater weight gain velocity (p = 0.02; p = 0.008) and MUAC velocity (p = 0.004, p = 0.03) when compared to RUTF at all ages and in the 24–59 months age group, respectively. There were no significant differences between treatment groups at time points in the other anthropometric outcomes. This investigation shows promising impact of stabilised rice bran as a prebiotic and nutrient-dense ingredient for inclusion into RUTFs that can improve child growth outcomes.