The main aims of the study were to quantify the burden of caries and determine factors associated with the highest risk for caries among 5–6-year-old schoolchildren in Sri Lanka. A cross-sectional descriptive study based on clinical oral examination, an interviewer-administered questionnaire for children and a parental self-administered questionnaire was conducted among, 5–6 years old (n = 403) in a selected province. Prevalence of caries was 56.7% (95% CI: 51.5–61.9%) and 3.4% (95% CI: 2.4–4.3%) for primary and permanent dentitions, respectively. A decayed, missing, and filled teeth (DMFT) index of 3.01 (95% CI: 2.61–3.41), significant caries index which is the DMFT of one-third of the study group with the highest caries score of 7.62 (95% CI of 7.34–7.9), prevalence of severely decayed untreated caries with pulpal involvement, ulcerations, fistula, and abscesses (PUFA) of 32.77% (95% CI of 32.32–33.22%), and a mean PUFA score of 1.26 (95% CI of 1.13–1.39) were observed for primary dentition. Although 43.3% of the sample did not have any caries, 10% had caries in all their primary molars, indicating a disproportionate treatment need. Having pulp exposed anterior teeth and father having three or more missing teeth were associated with having caries in all the primary molars. Severe burden of untreated caries at 5–6 years and polarization are seen as one in 10 study participants had all their primary molars decayed. While strengthening infant, toddler, and preschool oral health promotion, interventions targeting high-risk children are needed for reducing the caries burden.