Malaria is a major public health risk in Rwanda where children and pregnant women are most vulnerable. This infectious disease remains the main cause of morbidity and mortality among children in Rwanda. The main objectives of this study were to assess the prevalence of malaria among children aged six months to 14 years old in Rwanda and to identify the factors associated with malaria in this age group. This study used data from the 2017 Rwanda Malaria Indicator Survey. Due to the complex design used in sampling, a survey logistic regression model was used to fit the data and the outcome variable was the presence or absence of malaria. This study considered 8209 children in the analysis and the prevalence of malaria was 14.0%. This rate was higher among children aged 5–9 years old (15.6%), compared to other age groups. Evidently, the prevalence of malaria was also higher among children from poor families (19.4%) compared to children from the richest families (4.3%). The prevalence of malaria was higher among children from rural households (16.2%) compared to children from urban households (3.4%). The results revealed that other significant factors associated with malaria were: the gender of the child, the number of household members, whether the household had mosquito bed nets for sleeping, whether the dwelling had undergone indoor residual spraying in the 12 months prior to the survey, the location of the household’s source of drinking water, the main wall materials of the dwelling, and the age of the head of the household. The prevalence of malaria was also high among children living in houses with walls built from poorly suited materials; this suggests the need for intervention in construction materials. Further, it was found that the Eastern Province also needs special consideration in malaria control due to the higher prevalence of the disease among its residents, compared to those in other provinces.