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Administrative data show high vaccination coverage rates in Brazil, but there is no assessment of the validity and timeliness of dose administration, or whether the vaccination schedule is complete. This study assessed timely and updated coverage rates in children 12 to 24 months of age. This was a longitudinal population-based study in Araraquara, São Paulo State, a predominantly urban medium-sized municipality, using the Juarez System, an electronic immunization registry (EIR). Coverage rates were assessed in 49,741 children born from 1998 to 2013, a period in which five different vaccination schedules were used. Trends were estimated with the Prais-Winsten linear regression method. Updated coverage of the complete schedule varied from 79.5% to 91.3% at 12 months and from 75.8% to 86.9%, at 24 months. Timely coverage (all doses applied at the recommended ages, with no delays) ranged from 53.3% to 74% at 12 months and from 36.7% to 53.8% at 24 months. There was an upward trend in updated coverage at 24 months. The delays in relation to recommended age increased starting at six months and appeared to relate more to age than to the number of doses in the schedule. The proportion of invalid and late doses was lower than in other studies. Despite the increase in the number of doses in the vaccination schedule, the study showed high updated coverage rates and higher timely coverage than reported in the national and international literature; however, more effort is needed to increase timeliness. EIR proved relevant for assessing and monitoring vaccination coverage with more accurate analyses.