Background Dental caries and Obesity in children are issues of public health concern. Even though researching the relationship between these two noncommunicable diseases has been conducted for many years, the results remain equivocal. This paper aimed to examine the association between dental caries and obesity among 12-year-old schoolchildren living in war-affected environment in Benghazi. Methods A secondary analysis of a cross-sectional study was conducted to determine the prevalence of caries among 12-year-old school children in Benghazi in 2017 during the armed conflict that affected the city. The data extracted for the analysis included sociodemographic of the participants (gender, maternal education and school type), caries experience (DMFT index), and anthropometric measures (height in cm, weight in kg, BMI and Z score for BMI). Comparisons of anthropometric measures were conducted according to caries experience. Linear regression models were developed to determine the association between Body Mass Index and Z score as outcome variables, caries as an explanatory variable, and covariates (gender, maternal education and school type). Beta coefficient (β) and 95% confidence intervals were calculated. All statistical tests were conducted at p ≤ 0.05. Results There were 782 children with a mean (SD) BMI of 20.7 SD5.09 and an average z (SD) score of 0.56 SD1.51. Also, 159 (20%) children had obesity. No significant association was observed between caries and anthropometric measures. However, higher BMI was observed in children from a private school (p ≤ 0.001***), females (p ≤ 0.001***) and self-reported regular sugary drinks consumers (p ≤ 0.001***). Conclusion The present study shows no significant association between dental caries and anthropometric measures. However, the study findings support the notion of tackling sugar intake as a common risk factor for caries and obesity, which should be encouraged in the Libyan culture.