The prevalence of childhood obesity has increased over the years in the United States and contributed to a rise in metabolic syndrome and non-alcoholic fatty liver disease (NAFLD). Animal studies suggested the role of histamine blockade on mesenteric lymphatics tone, contributing to weight gain and hepatic steatosis. This study aimed to investigate an association between antihistamines (AH) use in children and obesity. A single-center retrospective cohort study on children with a diagnosis of NAFLD, followed in the gastroenterology clinic, was performed between January 2018 and April 2019. The demographics, medications, and body mass index (BMI) were assessed. Participants were divided into an AH group with documented use and comparison group, antihistamine naïve. Of the 32 participants in the study, 13 used AH, and 19 did not. Antihistamine users had a mean increase in BMI percentile per year of 1.17 compared to a decrease of 0.06 in comparison group (p = 0.0008). AH usage correlated with a mean increase in BMI z-score of 0.23 per year, as opposed to a decrease by 0.012 in comparison group (p = 0.0016). No difference was found in triglycerides (TG), glucose, and liver enzymes. AH use increases BMI percentiles and z-scores over time and is associated with obesity in children.