Objective: To estimate the prevalence and identify the determinants of non-prescription use of antibiotics for children in Mongolia. Methods: A community-based cross-sectional survey was undertaken in 10 subdistricts in Ulaanbaatar, Mongolia’s capital. We used a structured questionnaire to collect data from a random sample of 540 households with at least one child aged < 5 years. Logistic regression was used to identify factors associated with antibiotic misuse. Findings: Of 503 participating caregivers, 71% were mothers; 42.3% (95% confidence interval, CI: 37.8–46.9) of caregivers had used non-prescribed antibiotics to treat symptoms in their child during the previous 6 months. Symptoms commonly treated were cough (84%), fever (66%), nasal discharge (65%) and sore throat (60%). Amoxicillin was the most commonly used antibiotic (58%). Pharmacies were the main source (86%) of non-prescribed antibiotics. Non-prescribed use by mothers was significantly associated with keeping antibiotics at home (odds ratio, OR: 1.7; 95% CI: 1.04–2.79), caregiver self-medication (OR: 6.3; 95% CI: 3.8–10.5) and older child’s age (OR: 1.02; 95% CI: 1.01–1.04). Caregivers with a better knowledge of antibiotics were less likely to give children non-prescribed antibiotics (OR: 0.7; 95% CI: 0.6–0.8). Conclusion: The prevalence of non-prescribed antibiotic use for young children was high in Ulaanbaatar. Because such use leads to the spread of bacterial resistance to antibiotics and related health problems, our findings have important implications for public education and the enforcement of regulations regarding the sale of antibiotics in Mongolia.