BackgroundThe therapeutic feeding unit (TFU) provides comprehensive inpatient clinical care for children suffering from severe acute malnutrition (SAM) in three stages: stabilization, transition, and rehabilitation. During the transitional and rehabilitation phases, children receive either F-100 or ready-to-use therapeutic food (RUTF). Although both promote weight gain, RUTF is more energy dense than F-100. There is limited and contrasting evidence regarding their effect on recovery time. Therefore, this study aimed to assess the effect of RUTF on time to recovery among SAM children aged 6–59 months admitted to the TFU in Ethiopia.MethodsHealth Facility-based prospective cohort study was conducted among 476 children treated in three hospitals and four health centers in the Sidama region from September 2021 to January 2022. A structured questionnaire adopted from the Ethiopian national protocol for the management of SAM was used for data collection. Data were entered into EpiData version 3.1 and exported to SPSS version 20 for analysis. The Kaplan-Meir curve and log-rank test were used to compare time to recovery between children who received RUTF and F-100. Multivariable Cox proportional hazard analysis was conducted to assess the association between time to recovery and the type of therapeutic food, controlling for the confounding variables.ResultsThe median recovery time was significantly shorter in children receiving RUTF (7 days; 95% CI: 6.62–7.38) compared to F-100 (10 days; 95% CI: 8.94–11.06). Children below 24 months (AHR = 0.54, 95% CI: 0.42–0.69), dehydrated (AHR = 1.34, 95% CI: 1.07–1.75), edematous malnutrition (AHR = 1.29, 95% CI: 1.03–1.61), and anemic (AHR = 2.57, 95% CI: 1.90–3.48) during admission were associated with time to recovery.ConclusionsChildren who received RUTF recovered faster than children who received F-100. Administering RUTF to children below 24 months, who present with anemia and dehydration can improve their recovery rate and shorten their stay in the health facility.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12887-023-04168-x.