Home-based therapy with ready-to-use therapeutic food (RUTF) for the treatment of malnutrition has better outcomes in the research setting than standard therapy. This study examined outcomes of malnourished children aged 6-60 months enrolled in operational home-based therapy with RUTF. Children enrolled in 12 rural centres in southern Malawi were diagnosed with moderate or severe malnutrition according to the World Health Organization guidelines. They were treated with 733 kJ kg(-1) day(-1) of RUTF and followed fortnightly for up to 8 weeks. Staff at each centre followed one of three models: medical professionals administered treatment (5 centres), patients were referred by medical professionals and treated by community health aids (4 centres), or community health aids administered treatment (3 centres). The primary outcome of the study was clinical status, defined as recovered, failed, died or dropped out. Regression modelling was conducted to determine what aspects of the centre (formal training of staff, location along a main road) contributed to the outcome. Of 2131 severely malnourished children and 806 moderately malnourished, 89% and 85% recovered, respectively. Thirty-four (4%) of the moderately malnourished children failed, with 20 (2%) deaths, and 61 (3%) of the severely malnourished children failed, with 29 (1%) deaths. Centre location along a road was associated with a poor outcome. Outcomes for severely malnourished children were acceptable with respect to both the Sphere guidelines and the Prudhon case fatality index. Home-based therapy with RUTF yields acceptable results without requiring formally medically trained personnel; further implementation in comparable settings should be considered.