Introduction Electronic immunization registries (EIR) enable real-time monitoring of vaccination data and they are important for surveillance, disease control and relevant databases for research. While EIR has been used for decades in high-income countries, there are few experiences in middle-income countries. In Brazil, the EIR of the National Immunization Program has been implemented only from 2014. However, there were already some local initiatives, and the EIR of the city of Araraquara (SP) (Juarez System) is the oldest one. The Juarez System has individual vaccination data since 1986 and it is linked with the entire municipal healthcare network, which is responsible for feeding the system. It is an important tool to ensure high vaccination coverage in this city by identifying and calling children that are missing vaccination. Analyzes of inconsistencies are performed routinely in order to obtain high accuracy data. In addition, this EIR integrates in a single environment data of vaccination, notification of diseases, healthcare, laboratory and pharmaceutical assistance. The objective of this study was to analyze trend of vaccination coverage in Araraquara (SP), Brazil, using data from Juarez System, in 2000–2016 when the Brazilian Immunization Program introduced several vaccines in the basic schedule. Methods This is an ecological time series study. We analyzed data from 51,241 individuals born in 2000–2016 registered in the Juarez System. Araraquara is a medium-sized Brazilian city, with a population of 230,000 inhabitants and Human Development Index of 0.815. Immunopreventable diseases were controlled since decade of 1990 in this city. We evaluated vaccination coverage (number of vaccinated children/number of children registered in the system) per year of birth. We analyzed coverage of vaccination until 12 months for Bacillus Calmette–Guerin (BCG), hepatitis B, poliomyelitis, tetanus, diphtheria and pertussis (TDP), rotavirus, pneumococcus, meningococcus, yellow fever, hepatitis A and measles, mumps, and rubella (MMR) vaccines. We used the Prais–Winsten method for linear regression, with a significance level of 5%. Ethical clearance was provided by Ethics in Research Committee. Results Vaccination coverages were quite high. Almost all of them were above 95% in 2016. MMR, yellow fever and hepatitis A vaccination coverages were 92.3%, 93.5% and 89.1%, respectively, for 2015's birth cohort. BCG, TDP, poliomyelitis and hepatitis B vaccination coverages have increased about 0.5% per year. Rotavirus vaccination coverage has increased 1.2% (95% CI: 0.6–1.9%) per year since 2007. Yellow fever vaccination coverage has increased 2.5% (1.3–3.7%) per year since 2009. Pneumococcus, meningococcus and hepatitis A vaccination coverage remained stationary (P > 0.05). Data quality indicators showed that about 99.5% live births of Araraquara are registered in Juarez System and there is a low proportion of duplicate records (0.45%). Conclusions This study showed the potential of an EIR in the assessment of vaccine coverage in a medium-sized city of middle-income country. The improvement of the vaccination schedule over 17 years with the introduction of 10 new vaccines did not affect vaccination coverage trend and they are still increasing. Then, the control of immunopreventable diseases in Araraquara (since the 1990s) could be attributed not only to the good organization of the immunization program, but also to the good performance of the EIR, which ensures the adequate monitoring of vaccine coverage and calls for vaccination. In this way, the confidence and, consequently, the population's adherence to the immunization program are strengthened. Certainly, the Juarez System had its role in assisting the articulation of vaccination and surveillance activities, and offers a suitable database for research.