CD3 is an important membrane molecule of mature T cells. TCR‐CD3 complex plays important roles in the activation and signal transduction of T cells. In this study, the CD3ε (OnCD3ε) gene was cloned from Nile tilapia (Oreochromis niloticus), and its tissue distribution was detected by qPCR. The expression changes in CD3ε were analysed after three challenges (S. agalactiae, A. hydrophila and poly (I:C)) in vivo and in vitro. The open reading frame (ORF) of OnCD3ε contains 531 bp, encoding 176 amino acids, which found that OnCD3ε consists of conserved amino acid residues and motifs (cysteine residues, CXXC motif, immunoreceptor tyrosine‐based activation motifs and PxPDY). In addition, tissue distribution displayed that OnCD3ε has the highest expression in thymus and significant expression level in mucosal immune‐related tissues (intestine and gills). In vivo, all three challenges could significantly up‐regulate the expression of CD3ε in the head kidney and spleen. For further in vitro assays, after poly (I:C) stimulation, OnCD3ε appeared significant up‐regulation at 3 hr post stimulation, and two pathogenic bacteria also induce significant up‐regulation of OnCD3ε in spleen leucocytes (12 hr). These results suggested that OnCD3ε was likely to get involved in host immune response against pathogenic challenges.