Objective: Children's responses to food and their caregivers during normal developmental periods are known as feeding behavior. For the healthy development of these behaviors, parent and child relationships must also be healthy. Therefore, we aimed to investigate the effect of behavioral feeding problems on primary malnutrition (PM). Method: The Behavioral Pediatric Nutrition Assessment Scale (BPFAS) was administered to 300 malnourished and 300 control pediatric patients aged from 9 months to 4 years who were referred to our pediatric gastroenterology outpatient clinic. Pre- and posttreatment data were compared between the two groups. Results: There was no statistically significant difference between patients with and without malnutrition in terms of gender and age (p = 0.191, p = 0.128, respectively). Total behavioral frequency (TBF) and total behavioral problem (TBP) scores were significantly higher in the malnutrition group (p < 0.001). In the logistic regression analysis of risk factors that may affect malnutrition we found that a total TBF score of ≥85 increases the risk of developing malnutrition 3.731 times, a child TBF score of ≥62 increases it 2.644 times, and a parental TBF score of ≥21 increases it 4.82 times (p < 0.001). When anthropometric measurements and BPFAS scores of 127 PM patients who received behavioral therapy with enteral products and who attended follow-up were compared with their pretreatment data, there was a significant improvement (p < 0.05). Conclusion: Our study showed that behavioral feeding problems may increase the risk of PM and that behavioral therapy together with enteral products has a positive effect on treatment. Therefore, in addition to nutritional support in patients with PM, offering behavioral feeding therapy to parents will positively affect both the child's physical development and the relationship between the parents and their child.