Introduction: Monitoring of vaccination coverage is vital for the prevention and control of vaccine-preventable diseases. Electronic immunization registers have been increasingly adopted to assist with the monitoring of vaccine coverage; however, there is limited literature about the use of electronic registers in low- and middle-income countries such as Mongolia. We aimed to determine the accuracy and completeness of the newly introduced electronic immunization register for calculating vaccination coverage and determining vaccine effectiveness within two districts in Mongolia in comparison to written health provider records. Methods: We conducted a cross-sectional record review among children 2–23 months of age vaccinated at immunization clinics within the two districts. We linked data from written records with the electronic immunization register using the national identification number to determine the completeness and accuracy of the electronic register. Results: Both completeness (90.9%; 95% CI: 88.4–93.4) and accuracy (93.3%; 95% CI: 84.1–97.4) of the electronic immunization register were high when compared to written records. The increase in completeness over time indicated a delay in data entry. Conclusion: Through this audit, we have demonstrated concordance between a newly introduced electronic register and health provider records in a middle-income country setting. Based on this experience, we recommend that electronic registers be accompanied by routine quality assurance procedures for the monitoring of vaccination programmes in such settings.