A case-control study was conducted to determine the relationship between household livestock keeping and malnutrition levels of under-5 children. A questionnaire was used to capture data on the hypothesized risk factors. Fisher’s Exact test was used to determine associations between categorical variables and binary logistic regression analysis to determine predictors of malnutrition among under-5 children. A total of 145 households were sampled using a stratified random sampling method. About 72.4% (95% confidence interval [CI] = [63.9%, 81.0%]) of households in the study area kept livestock and the overall level of malnutrition was 34.5% (CI = [21.3%, 47.7%]). Livestock keeping among households that were cases was 31.4% (95% CI = [22.5%, 40.3%]) and slightly lower than those from households that were controls at 68.6% (95% CI = [57.9%, 59.3%]) although this was not statistically significant (p = .243). Crop farming alone was also found not to be significantly associated with malnutrition of under-5 children at household level (p = .447). However, mixed farming (growing crops and keeping livestock) at household level was found to be significantly associated with malnutrition levels of the under-5 children (p = .008). The level of mixed farming among the cases, 31.6% (95% CI = [17.7%, 45.5%]), was lower than those among the controls, which was 68.3% (95% CI = [59.1%, 77.5%]). There was no association between livestock keeping and malnutrition in both the cases and control groups. However, mixed farming (crop farming and keeping livestock) was associated with a significant reduction in malnutrition among under-5 children.