BACKGROUND: Electronic data capturing has the potential to improve data quality and user-friendliness compared to manually processed, paper-based documentation systems. The MyChild system uses an innovative approach to process immunization data by employing detachable vouchers integrated into a vaccination booklet which are then scanned and converted into individual-level health data. The aim was to evaluate the MyChild data capturing system by assessing the proportion of correctly processed vouchers and to compare the user-friendliness in term of time spent on documentation and health worker experiences with the standard health information system at health facilities in Uganda. METHODS: We used a mixed method approach. Documented data were manually copied and compared to processed health records to calculate the proportion of correctly registered vouchers. To compare time spend on documentation we did a continuous observational time-motion study and analyzed data using a Mann-Whitney U test. Semi-structured interviews were conducted to assess health workers' experiences and analyzed using conventional content analysis. Data was collected in 14 health facilities in two districts in Uganda using different systems. RESULTS: The MyChild system processed 97% (224 of 231) of the vouchers correctly. Recording using the MyChild system increased time spend on documentation of vaccination follow-up visits by 24 s compared to the standard system (02:25 vs. 02:01 min/child, Mann-Whitney U = 6293, n1 = 115, n2 = 151, p < 0.001 two-tailed, Z = - 3.861, r = 0.186). However, high variance between health centers using the same health information system suggests that documentation time differences can be attributed to other factors than the way information was processed. Health workers perceived both health management information systems as predominantly functional and easy to use, while the MyChild system achieved a higher level of satisfaction. CONCLUSIONS: The MyChild system electronically processes individual-level immunization data correctly without increasing significantly time spent on recording and is appreciated by health providers making it a potential solution to overcome shortcomings of present paper-based health information systems in health centers.