Abstract Background Traditional male circumcision (TMC) is primarily associated with a religious or cultural purpose and may lead to complications. To reduce risks of complication and long-term disabilities that may happen from circumcisions that are undertaken in non-clinical settings, information concerning TMC is very important. Therefore, this study is aimed at identifying spatial distribution of TMC and the factors associated with TMC in Ethiopia. Methods A secondary data analysis was conducted among 11,209 circumcised males using data from 2016 Ethiopian Demographic and Health Survey (EDHS). Global Moran’s I statistic was observed to check whether there was a significant clustering of TMC. Primary and secondary clusters of TMC were identified by fitting Bernoulli model in Kulldorff’s SaTScan software. Multilevel Generalized Linear Mixed effects Model (GLMM) was fitted to identify factors associated with TMC. Result The spatial distribution of TMC was nonrandom across the country with Global Moran’s I = 0.27 (p-value < 0.0001). The primary clusters of TMC were identified in the southern part of Oromia and Tigray, northern part of SNNPR, Amhara, Gambella and Benishangul regions. Current age, age at circumcision, ethnicity, religion, place of residence, wealth index, media exposure, sex of household head and age of household head were factors associated with TMC in Ethiopia. Conclusions The spatial distribution of TMC was varied across the country. This variation might be due to the diversity of culture, ethnicity and religion across the regions. Thus, there is a need to rearrange the regulations on standards of TMC practice, conduct training to familiarize operation technique and general hygiene procedures, and launch cross-referral systems between traditional circumcisers and health workers. While undertaking these public health interventions, due attention should be given to the identified clusters and significant factors.