BACKGROUND: The aim of this study was to assess the effectiveness of an EPI smartphone application (EPI app) on improving vaccination coverage in rural Sichuan Province, China. METHODS: This matched-pair cluster randomized controlled study included 32 village doctors, matched in 16 pairs, and took place from 2013 to 2015. Village doctors in the intervention group used the EPI app and reminder text messages while village doctors in the control group used their usual procedures and text messages. The primary outcome was full vaccination coverage with all five vaccines (1 dose of BCG, 3 doses of hepatitis B, 3 doses of OPV, 3 doses of DPT and 1 dose of measles vaccine), and the secondary outcome was coverage with each dose of the five individual vaccines. We also conducted qualitative interviews with village doctors to understand perceptions on using the EPI app and how this changed their vaccination work. RESULTS: The full vaccination coverage increased statistically significant from baseline to end-line in both the intervention (67 % [95 % CI:58-75 %] to 84 % [95 % CI:76-90 %], P = 0.028) and control group (71 % [95 % CI:62-79 %] to 82 % [95 % CI:74-88 %], P = 0.014). The intervention group had higher increase in full vaccination coverage from baseline to end-line compared to the control group (17 % vs 10 %), but this was not statistically significant (P = 0.164). Village doctors found it more convenient to use the EPI app to manage child vaccination and also reported saving time by looking up information of caregivers and contacting caregivers for overdue vaccinations quicker. However, village doctors found it hard to manage children who migrated out of the counties. CONCLUSIONS: This study showed that an app and text messages can be used by village doctors to improve full vaccination coverage, though no significant increase in vaccination coverage was found when assessing the effect of the app on its own. Village doctors using EPI app reported having improved their working efficiency of managing childhood vaccination. Future studies should be conducted to evaluate the impact of more integrated approach of mHealth intervention on child immunization. TRIAL REGISTRATION: Chinese Clinical Trials Registry (ChiCTR): ChiCTR-TRC- 13003960 , registered on December 6, 2013.