Children's self-control is associated with various behaviour-related health problems in childhood and later in life. However, studies on self-control and dental caries, strongly associated with toothbrushing or drinking and eating behaviour, are limited. We investigated the association between self-control and the number of decayed or filled primary teeth (dft) among first-grade children (6-7 years old) in Japan and evaluated the mediation effect of oral health behaviour on this association. A cross-sectional study of all first-grade elementary school children and their caregivers in Adachi ward (Tokyo) was conducted in 2015. Clinically determined dft status among children and caregiver-administered questionnaires on self-control was linked (n = 4291; valid response rate = 80.1%). Self-control was assessed by the following single question: "in the last month, was your child able to give up on things they want or do things that they do not like to do for better future outcomes?" Poisson regression analysis was conducted adjusting for age in months, sex, parental educational attainment and household income. Mediation analysis was performed to evaluate the mediation effects of toothbrushing frequency, frequency of drinking sugar-sweetened beverages and snack-eating habits on the association. Lower self-control was associated with higher dft after adjusting for all covariates (mean ratio = 1.09; 95% CI: 1.06, 1.12). Toothbrushing frequency, frequency of drinking sugar-sweetened beverages and snack-eating habits mediated 18.1%, 36.1% and 38.3% of the association between self-control and dft, respectively. Strengthening children's self-control might decrease their dental caries by improving their oral health behaviour.