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Background: After experiencing several cases of transfusion‐transmitted hepatitis E (TT‐HE) in Hokkaido, Northern Japan, hepatitis E virus (HEV) screening in blood donors, using a nucleic acid amplification test (NAT), was introduced in 2005. Study Design and Methods: The frequency of HEV RNA‐positive donations (2005–2019) was investigated, and the HEV RNA‐positive specimens were phylogenetically analyzed. In August 2014, the 20‐pooled NAT (20P‐NAT) was replaced with an individual‐NAT (ID‐NAT) system. Results: Until 2019, the frequency of HEV RNA‐positive donors was 0.011% (289/2,638,685) with 20P‐NAT and 0.043% (597/1,379,750) with ID‐NAT, and no TT‐HE cases were observed in Hokkaido. The prevalence among male, but not female donors, increased significantly between 2015 and 2019. Eighty‐nine percent of HEV isolates from donors were genotype 3 and the remainder were genotype 4, and many clusters existed in each genotype. ALT levels at the time of donation were significantly higher in donors with genotype 4. Four subgenotypes, namely 3a (37%), 3b (41%), 3e (6%), and 4c (10%), comprised 94% of the total. During this period, the most identified subgenotype, 3a, transitioned to 3b. Majority of the HEV strains within the same clusters were detected in the same geographical region around the same period. Many of the human HEV isolates were shown to coexist closely with animal HEV isolates phylogenetically. Conclusion: In Hokkaido, multiple divergent HEV strains have been circulating, and small outbreaks of hepatitis E have occurred in the last 15 years. The results suggested that HEV NAT can contribute significantly in ensuring safety during blood transfusions. [ABSTRACT FROM AUTHOR]