The general objective of this study was to assess the predicators of nutrition management failure among children under-five who participated in the nutrition program from 2012 up to 2015 in Nyamasheke District, Rwanda. The study included 169 children, out of which 78 were males and the remaining 91 were females. Of the children examined, 20.1% exhibited stunting growth of these 61.8% were females, 42.6% were underweight of these 51.4% were females and 10.1% were wasting of these 70.6% were males. Failure of nutritional management intervention was associated with both health system and family related factors. The common Health system predictors associated with failure of nutritional management programme were few activities related to the promotion of breastfeeding (OR: 5.0; 95 % CI: 1.56-16.2, P = 0.007), not following the Ministry of Health malnutrition management guidelines (OR: 5.85, 95% CI: 1.93417.69, P = 0.002), and poor knowledge about malnutrition management guideline (OR: 0.45, 95% CI: 0.21-0.99, P = 0.049). Family related predictors associated to the failure of nutritional management intervention include childhood illness such as fever (OR: 0.76, 95% CI: 0.36-1.61 P= 0.035), duration of breastfeeding (OR 0.7: 95% CI: 0.45-7.02 p = 0.035), number of meals per day (OR: 1.85 95% CI: 0.60-5.73; P = 0.002), and maternal age (OR: 1.96, 95% CI: 0.31-12.12; P = 0.027). These factors associated with failure of nutrition management should be considered in establishing effective measures for successful management and prevention of malnutrition.