This study identified caries-free associated factors and conducted multivariable projections of the caries-free prevalence until 2030 among six-, 12-, and 16-year-old schoolchildren in Malaysia. It was a secondary data analysis of caries-free prevalence and potential associated factors obtained from the Health Information Management System (HIMS), Department of Statistics Malaysia (DOSM), and Food Balance Sheets (FBS). Multiple linear regression and regression with ARMA errors were employed to determine the associated factors and predict the caries-free prevalence from 2019 or 2020 until 2030 for the six-, 12-, and 16-year-old groups, respectively. Gross Domestic Product (GDP) and household income, sugar consumption, and water fluoridation were significantly associated with caries-free status, with the most impactful in all age groups being water fluoridation. With the projected values of the associated factors, the caries-free prevalence in schoolchildren of all age groups in Malaysia is predicted to increase in the next decade. Similar to the past decade, the prevalence trend will remain the highest among the 12-year-olds and the lowest among six-year-olds. Caries-free prevalence was predicted to increase by 9.10%, 15.52%, and 15.10% in the six-, 12-, and 16-year-old groups, respectively. The prevalence multiplied the highest at four times greater than in the past ten years among 16-year-olds, compared with less than 2% in the six- and 12-year-old groups. In conclusion, by factoring in economic factors, sugar consumption, water fluoridation, and age groups, the caries-free prevalence of schoolchildren in Malaysia is projected to increase at different rates in the next decade until 2030. Thus, strategic oral health plans to recognise effective promotion programmes and strengthen others for each age group are crucial.