In developing countries including Ethiopia stunting remained a major public health burden. It is associated with adverse health consequences, thus, investigating predictors of childhood stunting is crucial to design appropriate strategies to intervene the problem stunting. The study uses data from the Ethiopian Demographic and Health Survey (EDHS) conducted from January 18 to June 27, 2016 in Ethiopia. A total of 8117 children aged 6–59 months were included in the study with a stratified two stage cluster sampling technique. A Bayesian multilevel logistic regression was fitted using Win BUGS version 1.4.3 software to identify predictors of stunting among children age 6–59 months. Adjusted odds ratio (AOR) with 95% credible intervals was used to ascertain the strength and direction of association. In this study, increasing child’s age (AOR = 1.022; 95% CrI 1.018–1.026), being a male child (AOR = 1.16; 95%CrI 1.05–1.29), a twin (AOR = 2.55; 95% CrI 1.78–3.56), having fever (AOR = 1.23; 95%CrI 1.02–1.46), having no formal education (AOR = 1.99; 95%CrI 1.28–2.96) and primary education (AOR = 83; 95%CrI 1.19–2.73), birth interval less than 24 months (AOR = 1.40; 95% CrI 1.20–1.61), increasing maternal BMI (AOR = 0.95; 95% CrI 0.93–0.97), and poorest household wealth status (AOR = 1.78; 95% CrI 1.35–2.30) were predictors of childhood stunting at individual level. Similarly, region and type of toilet facility were predictors of childhood stunting at community level. The current study revealed that both individual and community level factors were predictors of childhood stunting in Ethiopia. Thus, more emphasize should be given by the concerned bodies to intervene the problem stunting by improving maternal education, promotion of girl education, improving the economic status of households, promotion of context-specific child feeding practices, improving maternal nutrition education and counseling, and improving sanitation and hygiene practices.