We assessed a nutritional support intervention in malnourished HIV-infected children in a HIV-care program of the University Hospital Gabriel Touré, Bamako, Mali. All HIV-infected children younger than 15 years were diagnosed for malnutrition between 07 and 12, 2014. Malnutrition was defined according to the WHO growth standards with Z-scores. Two types were studied: acute malnutrition (AM) and chronic malnutrition (CM). All participants were enrolled in a 6-month prospective interventional cohort, receiving Ready-To-Use Therapeutic Food, according to type of malnutrition. The nutritional intervention was offered until child growth reached -1.5 SD threshold. Six-month probability to catch up growth (>-2 SD) was assessed for AM using Kaplan-Meier curves and Cox model. Among the 348 children screened, 198 (57%) were malnourished of whom 158 (80%) children were included: 97 (61%) for AM (35 with associated CM) and 61 (39%) with CM. Fifty-nine percent were boys, 97% were on antiretroviral therapy, median age was 9.5 years (Interquartile Range: 6.7-12.3). Among children with AM, 74% catch-up their growth at 6-month; probability to catch-up growth was greater for those without associated CM (adjusted Hazard Ratio = 1.97, CI 95%: 1.13 to 3.44). Anemia decreased significantly from 40% to 12% at the end of intervention (P < 0.001). This macronutrient intervention showed 6-month benefits for weight gain and reduced anemia among these children mainly on antiretroviral therapy for years and aged greater than 5 years at inclusion. Associated CM slows down AM recovery and needs longer support. Integration of nutritional screening and care in the pediatric HIV-care package is needed to optimize growth and prevent metabolic disorders.