Background: The persistently high prevalence of undernutrition in Cambodia, in particular stunting or chronic malnutrition, calls for innovative investigation into the risk factors that affect children’s growth during critical phases of development. Methods: Secondary data analysis was performed on a subgroup of children who were present at two time points within the Cambodian Health and Nutrition Monitoring Study (CAHENMS) and who were less than 24 months of age at the nominated baseline. Data consisted of parent interviews on sociodemographic characteristics and feeding practices, and clinical measures for anthropometric measures and dental status. Logistic regression modelling was used to examine the associations between severe dental caries (tooth decay)—as indicated by the Significant Caries Index—and the presence of new cases of stunting malnutrition at follow-up. Results: There were 1595 children who met the inclusion criteria and 1307 (81.9%) were followed after one year. At baseline, 14.4% of the children had severe dental caries, 25.6% presented with stunted growth. 17.6% of the children transitioned from healthy status to a low height-for-age over the observation period. Children with severe dental caries had nearly double the risk (OR = 1.8; CI 1.0–3.0) of making that transition. Conclusion: Severe caries experience was associated with poorer childhood growth and, as such, could be an underinvestigated contributor to stunting.