Newcastle disease virus (NDV) is a highly lethal and contagious viral pathogen; it is also a potent oncolytic virus that selectively replicates in tumor cells. NDV demonstrates high replication efficiency in avian and tumor cells, causing various types of cell death, including ferroptosis, necrosis, apoptosis and autophagic cell death, with apoptosis being the most thoroughly studied. Organelles play critical and distinctive roles in the regulation and execution of apoptosis. However, the involvement of peroxisomes, an important organelle that regulates redox balance and lipid biosynthesis, in virus-induced apoptosis remains unclear. Our findings reveal that NDV infection promotes the downregulation of several peroxisome biogenesis factors (PEXs) at the mRNA level. Peroxisomal biogenesis factor 5 (PEX5), a critical peroxisomal shuttle protein, was identified to be significantly downregulated at both the mRNA and protein levels. Further, gain- and loss-of-function experiments demonstrated the negative regulation of NDV-induced apoptosis by PEX5. In addition, PEX5 inhibits NDV-induced apoptosis by regulating the anti-apoptotic protein B-cell lymphoma-2 (Bcl-2) expression. These findings reveal a novel mechanism by which NDV-induced apoptosis is modulated through the downregulation of PEXs, particularly PEX5, shedding light on the potential role of peroxisome in apoptosis regulation in response to virus infection.