Highly pathogenic avian influenza (HPAI) is a serious viral infection that causes massive economic losses in poultry. The current study investigated the HPAI virus prevalence in commercial broiler chicken flocks from 2019 to 2022. Organ samples, including trachea, cecal tonsils, spleen, brain, as well as tracheal and cloacal swabs, were harvested from 111 problematic broiler chicken flocks that suffered from variable mortalities accompanied with respiratory signs (103 H5-vaccinated and 8 nonvaccinated flocks) in Egypt during the observation duration. Molecular tools were used to analyze the samples, including real-time reverse transcription-polymerase chain reaction (rRT-PCR) and sequence analysis of some PCR positive strains. The results indicated that 24 flocks were positive for HPAI H5N8, representing 21.6%, with 22.3% (23/103) prevalence and 12.5% (1/8) detection in vaccinated and nonvaccinated flocks, respectively, and they were almost detected in the autumn and winter seasons. Phylogenetic evaluation of the hemagglutinin (HA) gene showed that the 6 Egyptian strains were clustered in clade 2.3.4.4b and allocated into 2 groups (I and II). The samples recovered in 2019 were clustered in new subgroup A, and samples recovered in 2020 to 2022 were clustered in new subgroup B with 10 nucleotide mutations (R72S, A83D, T140A). In conclusion, HPAI H5N8 is a serious threat even in vaccinated birds; to control such problems, periodic molecular monitoring with vaccine efficacy evaluation and the use of preventive strategies are recommended.