The prevalence of malnutrition among children under five is alarmingly high in Pakistan. However, there are ready-to-use therapeutic foods (RUTF) available which may be used to treat children with severe acute malnutrition (SAM). This study aims to assess the efficacy of prebiotics as a synergistic additive to RUTF to enhance blood parameters and anthropometric measurements in children with uncomplicated SAM living in Southern Punjab, Pakistan. A double-blind parallel treatment randomized controlled trial was conducted on 204 children aged 6–59 months. Participants were randomized and allocated to the placebo (n= 102) or experimental arms (n= 102) in a 1:1 ratio. One group of children was provided with RUTF and 4 g prebiotics, while the other group was given RUTF and starch as a placebo. Participants recruited for both arms were given treatment for eight weeks, and then their biochemical and anthropometric outcomes were evaluated. A substantial difference between the mean weight, mid-upper-arm circumference, haemoglobin, haematocrit, platelet count, mean corpuscular volume, mean corpuscular haemoglobin, and albumin was revealed. During the two-month follow-up phase of the trial, children who were enrolled in the treatment group gained about 20% of their initial weight (pre-study mean weight = 5.44 ± 1.35 kg; post-study mean weight = 6.53 ± 1.45 kg). The analysis showed a significant difference (p< 0.005) between the control and treatment groups for MUAC and complete blood counts. Conclusively, supplementation with RUTF and prebiotics has proven to be an efficient, effective, and safe therapy for children suffering from SAM to improve their growth and development indicators and reduce the dangers of malnutrition in comparison to RUTF alone.