This study assessed the association between the eruption stage of permanent second molars and occlusal caries activity among 12-year-old schoolchildren from South Brazil. A cross-sectional study was performed in Porto Alegre using a multistage probability sampling strategy to select a representative sample. Clinical examination was conducted to assess the eruption stage of permanent molars, Gingival Bleeding Index, and, after tooth cleaning and drying, caries experience (noncavitated and cavitated lesions, including caries activity assessment). Data were collected on sex, socioeconomic status, mother’s education, brushing frequency, and consumption of soft drinks. Generalized estimating equations were used to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Overall, 983 schoolchildren with 3,071 second molars were available for analysis. Whereas active caries was observed in 6.6% of fully erupted permanent second molars, caries affected 26.2%, 29.6%, and 18.2% of erupting molars classified as stages 1, 2, and 3, respectively: stage 1, partially erupted occlusal surface; stage 2, fully erupted occlusal surface, <1/2 crown exposed; and stage 3, fully erupted occlusal surface, >1/2 crown exposed. After adjusting for socioeconomic and behavioral variables, partially erupted molars were significantly more likely to present active caries lesions than molars in full occlusion: stage 1, OR = 4.99 (95% CI = 3.38, 7.38); stage 2, OR = 5.18 (95% CI = 3.14, 8.53); stage 3, OR = 3.20 (95% CI = 2.21, 4.64). Similar results were found when clinical variables were included in the adjusted model. In conclusion, most occlusal caries lesions tend to arrest/revert when teeth reach the occlusal plan; however, an important proportion of these lesions remains active and in need of proper management. Children at risk should be targeted with preventive and minimally invasive strategies.