Background Under five years of age child mortality rates and the violence against women are prevalent in Rwanda. The violence is known to negatively affect the women’s and their children’s health. This study aimed to examine the association between maternal experience of lifetime intimate partner violence and symptoms of common illnesses (fever, diarrhea, cough, breathing problems) among the children under five years of age in Rwanda. Methods The study was a cross-sectional, based on the data of 2019 –20 Rwanda’s Demographic Health Survey, including 1,290 women and their children. To examine the association between physical, sexual and psychological intimate partner violence and the symptoms of common illnesses, bivariate analysis was performed, followed by logistic regression, where models were adjusted for potential confounders. Results Among the mothers, 36% had experienced physical, 14.7% sexual, and 33.7% psychological intimate partner violence. Around 43% of their children had had symptoms of common illnesses within two weeks before the data collection. In adjusted regression analysis, the experience of physical (OR 1.79, CI 1.41 – 2.27), sexual (OR 1.68, CI 1.22 – 2.30) and psychological intimate partner violence (OR 2.08, CI 1.63 – 2.65) were significantly associated with symptoms of common illnesses among children under five years of age. Conclusion This study showed that maternal experience of lifetime intimate partner violence increases the likelihood of their young children having symptoms of common illnesses in Rwanda. The finding suggests the importance of investing in strategies against intimate partner violence to lower the mortality rates of children within the country.