Background: The health seeking behavior in Kenya raises concerns in malaria case management at the private sector. Adherence to the national guidelines for the diagnosis, treatment and prevention of malaria is key in management of the disease. Presumptive treatment remains a major challenge in Kenya, especially in the private sector, with major gaps in literature identified on predictors of this treatment. Mixed-effects regression modelling considers county clustering, is more accurate in prediction and is more efficient and flexible. Methods: The study design was a cross-sectional, nationally representative, retail outlet survey secondary data analysis. The study populations included the health care providers in the retail outlets sampled randomly in both the rural and urban settings in Kenya. The primary outcome of interest was the proportion of health care providers who treated patients presumptively. Multivariable analysis was conducted for the significant variables, adjusting for clustering at the county level to determine the predictors of presumptive treatment. The best fitting model was examined using the Akaike Information Criterion (AIC). Results: Out of the 333 health care providers who treated patients, 190 (57%) treated patients presumptively. From the mixed effects logistic regression model, the predictors of presumptive treatment of uncomplicated malaria were case management training (AOR = 0.44; 95% CI = (0.18 – 1.09)), asked signs or symptoms (AOR = 0.19; 95% CI = (0.10 - 0.37)) and results presented (AOR = 0.08 95% CI = (0.03 - 0.19)). Conclusions: Presumptive treatment of uncomplicated malaria remains a challenge in the private retail sector. Malaria case management training and health care providers asking of signs and symptoms and results presented predicts presumptive treatment. To address the issue of presumptive treatment of Malaria, strengthening of malaria case management training is key for health care providers in the private sector.