Background: Toothache is a common condition among children that often leads to school absenteeism. However, there is limited information on the prevalence of toothache and its associated factors in Iranian children. Objectives: This study aimed to assess the prevalence of toothache and related factors in 12-year-old Iranian children. Methods: This was a cross-sectional population-based study. Multistage cluster sampling was used to recruit the participants from three provinces (Tehran, Kerman, and Fars). Parents of 1,468 students aged 12 years completed a valid questionnaire that assessed their socioeconomic status and the children’s oral hygiene behavior, toothache, and absenteeism in the last 6 months. A multivariate random effects logistic regression model was adopted to analyze the effect of demographic, geographic, and oral hygiene practice factors on toothache prevalence. Results: The prevalence of toothache in children was high, with 41% (95% CI = 38.4, 43.5) of the children reporting toothache. Of the children who had a toothache, 12.8% missed 1 to 7 school days. The prevalence of toothache was significantly higher in children living in cities compared to those living in towns (P < 0.001). Additionally, toothache prevalence had a significant association with the fathers’ educational level (P = 0.003) and the children’s toothbrushing and flossing practices (P < 0.001). Conclusions: The high prevalence of toothache among Iranian children highlights the need for effective health interventions to control this condition. These interventions can focus on improving oral hygiene practices and increasing access to dental care in both urban and rural areas. Moreover, targeting families with lower educational levels could be an effective approach to reducing the prevalence of toothache in children.