The present study investigated anevaluation of the efficacy of a school-based deworming program on the nutritional status of school children (59–119 months) in Barangay San Lucas 1, San Pablo City, Laguna. Through random sampling, 175 school children participated in the study. Anthropometric measurements were obtained, and participants’ primary caregivers were asked to complete a child eating behavior questionnaire (CEBQ). The study revealed that most of the study participants were from low-income households, and that the mother-reported and observed children’s desire to drink had the highest attained mean among all the subscales, followed by the enjoyment of food. Meanwhile, the subscale that had the lowest mean included emotional overeating and food responsiveness. Before deworming, the prevalence of wasting and underweight were both “very high” (25.71% and 28.0%, respectively), while stunting prevalence was “low” (9.14%). After deworming, there was a significant difference in the proportion of wasting (x2 = 26.1; p < 0.001) and stunting (x2 = 29.4; p < 0.001). However, there was no significant difference in stunting prevalence before and after deworming (x2 = 0.12; p < 0.001). It was concluded that deworming influences wasting (low weight-for-height) and underweight (low weight-for-age) by lowering its prevalence after intervention; for stunting, tt was also found that correlations between sociodemographic profile and nutritional status, sociodemographic profile and child eating behavior, child eating behavior and deworming, and deworming and nutritional status were significant at p<0.01. However, there is no sufficient evidence to say that there was significant difference before and after deworming across all eating behavior subscales.