As an important generator of reactive oxygen species (ROS) in eukaryotic cells, nicotinamide adenine dinucleotide phosphate (NADPH) oxidase (NOX) is essential to antimicrobial host defense. AjNOX, a member of the NOX family, was identified in Apostichopus japonicus during the current investigation. It encodes a polypeptide with 571 amino acids, and it has an open reading frame of 1716 bp. The inferred amino acid sequence of AjNOX includes a transmembrane domain, a ferric reductase domain, a flavin adenine dinucleotide-binding-8 domain, and a NADPH-binding-6 domain. AjNOX shares 53.03%–42.39% sequence homology with other NOX proteins found in vertebrates and invertebrates in accordance with multiple sequence alignment. AjNOX was found in close proximity to the sea urchin SpNOX and the vertebrate NOX1–3 on the phylogenetic tree. The AjNOX gene was expressed in all of the test tissues including the body wall, muscle, intestine, respiratory tree, and coelomocytes. After being challenged with Vibrio splendidus, sea cucumber coelomocytes showed a remarkable increase in the protein and mRNA levels of AjNOX. ROS was produced less remarkably in coelomocytes as a result of AjNOX RNA interference. When the expression of AjNOX was suppressed by siRNA or inhibitor, the ability of coelomocytes to remove bacteria was drastically decreased. Reducing AjNOX-derived ROS decreased the production of inflammatory cytokines and coelomocyte apoptosis. All of these findings indicate that AjNOX may be crucial to the antibacterial immune response against the invasive pathogen V. splendidus in sea cucumbers A. japonicus.