Duck hepatitis A virus (DHAV) causes acute hepatitis and mortality, resulting in high economic losses in the duck farm industry. The current study describes the outbreak of DHAV in vaccinated duck farms in North Egypt during 2019 and molecular characterization of the 3′ untranslated region (UTR) and viral protein VP1 genes. The 30 samples were collected from 7- to 28-day-old commercial Pekin ducks that showed a history of nervous signs and sudden deaths and were on farms in 6 governorates. DHAV was typed by reverse transcription–polymerase chain reaction (RT-PCR) for 3′ UTR and VP1 genes and revealed 20 positive farms, with the first detection of DHAV genotype 3 (DHAV-3) in 18 samples and the classic DHAV-1 in 2 samples. The phylogenetic analysis of VP1 and 3′ UTR genes of the nine selected strains representative of six governorates revealed that seven strains were clustered with DHAV-3 Chinese and Korean-Vietnamese strains within different subgroups with 92.4%–93.7% amino acid identity; such strains were distinguishable from the vaccine strain of DHAV-1 used in Egypt with 74.4% amino acid identity. The other strains were closely related to the DHAV-1 Asian strain and the vaccine strain used in Egypt with 98.7%–99.6% amino acid identity for the VP1 gene with different clustering than that of recently isolated DHAV-1 Egyptian strains. The VP1 gene of DHAV-3 had 1 hypervariable region (HVR) with 10 amino acid mutations compared with DHAV3/DN2/Vietnam/2011, but DHAV-1 had 3 HVRs with 1 amino acid mutation in HVRII compared with the DHAV-1 vaccine strain. In conclusion, a new introduction of DHAV-3 with the classical DHAV-1 was recorded in Pekin duck farms in North Egypt that is genetically distant from the vaccinal strain.