Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis, responsible for large outbreaks in resource limited countries. The virus belongs to the genus Orthohepevirus which is subdivided into eight distinct genotypes (HEV-1 to HEV-8). Human disease transmission is mostly through the faecal-oral route. However, zoonotic transmission could also occur. In the Niger Republic, the first documented HEV outbreak was recorded in 2017 around displaced persons camps in the Diffa region across the Lake Chad basin, resulting in 736 confirmed cases and 38 (1.9%) deaths. Since then, sporadic cases were annually reported despite the lack of specific surveillance. Overall, from 2017 to 2023, a total of 2820 HEV suspected cases were sampled, out of which 906 (32.12%) were confirmed positive by either qRT-PCR and/or IgM ELISA. Out of the 21 characterized isolates, we identified 15 sequences belonging to the genotype 1e and 6 sequences to the genotype 2b. The newly characterized sequences from Niger clustered with those circulating in neighbouring countries, suggesting a cross-border virus circulation. The co-circulation of HEV genotypes 1 and 2 is an indicator of the probable virus transmission through contaminated water sources. Thus, there is a crucial need to improve the preparedness and implement an active and integrated community-based surveillance. This should include field testing for rapid detection and characterization of HEV as well as actions for disease containment, strengthening of hygiene measures and community-based sensitization for behavioural changes.