Rotavirus is the most common cause of severe gastroenteritis in children worldwide. This retrospective, cross-sectional study was undertaken in a sentinel hospital that provides the only pediatric beds for the local population with an average of 4,400 children aged <5 years and determined the incidence of rotavirus hospitalizations. Medical charts that recorded acute gastroenteritis cases occurring in children aged <5 years living in the cites of Yuri-Honjo or Nikaho, Akita, Japan between 2001 and 2011 were retrieved and examined to enumerate rotavirus antigen-positive hospitalizations. Of the 1,596 acute gastroenteritis cases retrieved, antigen detection was performed in 834 cases, and 387 were positive; hence, the crude annual incidence rate of rotavirus hospitalizations was 8.8 per 1,000 person-years. The adjusted annual incidence rate of rotavirus hospitalizations was 13.7 per 1,000 person-years when untested samples collected during the peak season were extrapolated to the same rotavirus detection proportion as the tested samples (58.9%). We confirmed a high incidence of rotavirus hospitalizations in Akita Prefecture and revealed a considerable degree of annual fluctuation in the rotavirus hospitalization rates, which exceeded the degree of stochastic fluctuation. Thus, caution must be exercised when interpreting the impact of a rotavirus vaccine on the reduction of the number of rotavirus hospitalizations.