Entamoeba histolytica is an important cause of diarrheal disease worldwide; however, its contribution to diarrheal illness in Mongolia remains poorly understood. We investigated the seroprevalence of E. histolytica among hospitalized patients with diarrhea, characterized bacterial and viral enteric pathogens in stool specimens from E. histolytica-seropositive patients, and evaluated associated environmental and behavioral risk factors. A hospital-based cross-sectional study was conducted among 83 patients hospitalized with diarrhea at the National Center for Communicable Diseases, Ulaanbaatar, between July 16 and August 20, 2025. Serum samples were tested for E. histolytica-specific IgG antibodies by ELISA. Stool specimens from seropositive patients were further analyzed for bacterial and viral enteric pathogens using multiplex PCR assays. Demographic, environmental, and behavioral risk factors were assessed using structured questionnaires. Preschool-aged children constituted the largest proportion of all hospitalized patients with diarrhea (43.4%, P=0.001). E. histolytica-specific IgG antibodies were detected in 7 of 83 participants (8.4%). Among E. histolytica-seropositive patients, bacterial enteric pathogens were detected in 71.4% (5/7) of stool specimens, including enterotoxigenic, enteroaggregative, and enteropathogenic Escherichia coli. No viral pathogens were detected. Multivariable logistic regression analysis showed that consumption of unwashed fruits and vegetables was significantly associated with E. histolytica seropositivity (adjusted odds ratio, 6.2; 95% confidence interval, 1.6–15.2; P=0.026). These findings highlight the need for improved laboratory diagnostic capacity and enhanced food hygiene interventions to facilitate the diagnosis and prevention of amoebic diarrhea.