Pneumonia remains an important cause of morbidity and mortality among children in low- and middle-income countries. Poor outcomes are associated with undernutrition. Nutritional supplementation may be beneficial. We examined the effect of supplementation with lipid-based ready-to-use therapeutic food (RUTF) on the body composition of children with severe pneumonia. Non-severely malnourished children (6–59 months) with severe pneumonia enrolled into the Children’s Oxygen Administration Strategies and Nutrition trial in Uganda and Kenya, and randomized to receive a diet supplemented with RUTF (500 Kcal/day) for 56 days versus usual diet alone (control) were included. We assessed arm anthropometry and bioimpedance analysis at admission and days 28, 90, and 180 of follow-up. We used mixed effects linear regression to compare body composition between groups. We included 737 participants (369 in intervention; 368 in control group). The median age was 16 months (IQR; 9, 26), and 58.1% were male. Overall, baseline mean arm fat area (AFA), arm muscle area, and arm muscle circumference were 5.8 ± 1.8 cm2, 11.6 ± 2.3 cm2, and 12.3 ± 1.2 cm2, respectively. The mean fat mass and fat-free mass calculated in 116 participants were 5.5 ± 1.5 kg and 5.5 ± 1.5 kg, respectively. There were modest increases in most body composition parameters. RUTF significantly increased AFA at days 28 and 90 but not at day 180 (P-value = .03, .02, and .99, respectively). RUTF did not change other body composition parameters. Despite initial increases in AFA, RUTF did not change the body composition of children with severe pneumonia.