The Indonesian family life survey (IFLS) is used for formulating various government policies. Our preliminary study using data from the IFLS showed increase in the prevalence of toothache from 2007 to 2014. Hence, a need to analyse the factors associated with toothache using structural equation modelling (SEM) for identifying the direct and indirect association of factors with toothache was evident. The objective of this study is to analyse the complex relationships between toothache and its associated risk factors. This cross-sectional study was conducted on the data obtained from the IFLS in 2014. The IFLS data pertaining to toothache and its prevalence were analysed using the STATA software, and the multifaceted relationship was analysed using SEM. The prevalence of toothache among Indonesian children was 15.55% (1,959 of 12,595). SEM showed the direct association between toothache and age (p < 0.001) and parent awareness of children's health conditions (p < 0.005) and food consumption frequency (p < 0.001). Parents' education level and residential area showed an indirect association with toothache, mediated by socio-economic status and parent awareness of children's health conditions (p < 0.001). We identified the multifaceted relationship between toothache and the social covariates. Parents' awareness of their children's health conditions mediated several indirect associations, highlighting its importance.