Background and objective Healthcare-seeking behavior for children is crucial for reducing disease severity. Such behavior can improve child health outcomes and prevent child morbidity and mortality. The present study sought to analyze the determinants of mothers’ engagement in healthcare-seeking behavior for children with common childhood diseases, focusing on mothers of children aged 0–59 months in Indonesia. Methods This cross-sectional study comprised a secondary data analysis using the 2002–2017 Indonesia Demographic and Health Survey (IDHS) databases. We included all women surveyed aged 15–49 years old who had children under five years of age. We weighted the univariate, bivariate, and multivariate logistic regression analysis of healthcare-seeking behavior for children aged 0–59 months. Results We analyzed data for 24,529 women whose children were under five years of age at the time of survey. Common diseases, such as diarrhea, fever, and acute respiratory infection (ARI) were the most frequently cited reasons for healthcare-seeking behavior. During 2002–2017, the proportion of mothers seeking healthcare for their children with diarrhea increased from 67.70% to 69.88%, that with fever increased from 61.48% to 71.64% and that ARI increased from 64.01% to 76.75%. Multivariate analysis revealed that child’s age, child’s birth order, mother’s education, ability to meet expenses, distance to nearest healthcare facility, wealth index, place of residence, and region of residence, were significantly associated with healthcare-seeking behavior. Conclusion Various individual and environmental-level factors influence healthcare-seeking behavior for childhood diseases. Available, accessible, and affordable health service facilities are recommended to assist socio-economically and geographically disadvantaged families.