Simple, systematic, and sustainable passive surveillance systems for vaccine-preventable diseases (VPDs) should be useful to quantify the clinical and economic burden in a timely manner with minimum investment. This pilot study evaluated the usefulness of nationwide administrative databases (a hospital-based administrative database and an insurance claims database) for such passive surveillance of children hospitalized for VPDs using rotavirus gastroenteritis (RGE) as an example. Two rotavirus vaccines were launched in November 2011 and July 2012 in Japan. We assessed changes in the proportion of RGE hospitalizations among all-cause hospitalizations (N = 506,524) from the hospital database (April 2008–December 2016) and annual RGE hospitalization rates from the insurance claims database (January 2011–December 2016, n of beneficiaries = 460,585) in children aged <6 years. A total of 12,599 hospitalizations in 12,366 patients were associated with RGE from the hospital database. Similarly, 2038 patients had 2137 RGE-related hospitalizations from the insurance claims database. From 2009 to 2013, the proportion of RGE hospitalizations increased from 2.2% (95% confidence interval, 1.8–2.6) to 3.9% (3.7–4.0), then decreased and remained consistently low from 2014 (1.9% 1.8–2.0) to 2016 (2.2% 2.1–2.3). The RGE hospitalization rate decreased sharply in 2014, ranging between 2.85 and 3.52 during 2011–2013 to 0.97 (0.84–1.09) in 2014, and remained low through 2016 (1.18 1.04–1.32). In conclusion, we observed changes in RGE hospitalizations over time, without requiring additional data entry by clinicians. Nationwide administrative databases can be useful tools for passive surveillance of VPDs in Japan.