Background In 2017, a diphtheria outbreak occurred in several provinces in Indonesia. The aim of this study was to identify predictors of mortality outcome of pediatric patients with clinical diphtheria. Methods A retrospective cohort study was conducted using patient medical records at five referral hospitals in the Province of Jakarta and one in Tangerang District, Banten Province during January 2017 to 31 August 2018. All children in the age group of 1-18 years old discharged with diagnosis of clinical diphtheria formed the study group. All anonymized patient data were evaluated for demographic issues, clinical features, immunization status, complication, laboratory profiles and outcome. Results A total of 283 patients with clinical diphtheria were included in the study group with case fatality rate of 3.5%. All mortal patients had the complication of myocarditis. Regression analyses revealed factors for predicting mortality. Incomplete primary diphtheria toxoid immunization, stridor, bull neck, leukocytosis ≥15 ×109 cells/L and thrombocytopenia ≤150 x109 cells/L in each combination for 2 predictors modeling were correlated with death. Conclusions We report key predictors of mortality in pediatric patients with clinical diphtheria. The presence of these features when admitted to the hospital must be taken into account, because they can lead to fatal outcome.