Stunting prevalence in Rwanda is still a major public health issue, and data on stunting is needed to plan relevant interventions. This data, collected in 2015, presents complementary feeding practices, nutrient intake and its association with stunting in infants and young children in Musanze District in Rwanda. A household questionnaire and a 24-h recall questionnaire were used to collect the data. In total 145 children aged 5–30 months participated in the study together with their caregivers. The anthropometric status of children was calculated using WHO Anthro software  according to the WHO growth standards . The complementary feeding practices together with households’ characteristics are reported per child stunting status. The nutrient intake and food group consumption are presented per age group of children. Also, the percentage contribution of each food groups to energy and nutrient intake in children is reported. The data also shows the association between zinc intake and age groups of children. Using multiple linear regression, a sensitivity analysis was done with height-for-age z-score as the dependent variable and exclusive breastfeeding, deworming table use, BMI of caregiver, dietary zinc intake as independent variables. The original linear regression model and a detailed methodology and analyses conducted are presented in Uwiringiyimana et al. .