In the past decade, immunotoxins have been developed for targeted cancer therapy. These chimeric proteins consisting of a targeting moiety of monoclonal antibody or ligand binding to cancer cell surface receptor and potent proteins such as bacterial and plant-derived toxins have demonstrated a powerful ability to kill cancer cells. Chemical conjugation or fusion protein methods have been explored as means to obtain immunotoxins. However, most chemical conjugation methods result in heterogeneous products, and the fused forms of immunotoxin have been reported only for antibody fragments rather than full-length ones. Here, we report a site-specifically conjugated immunotoxin composed of Herceptin, targeting the HER2/neu receptor, and PE24 derived from Pseudomonas exotoxin A. the conjugation was performed by THIOMAB technology and method to incorporate unnatural amino acids into protein. The THIOMAB technology allows products to avoid heterogeneity through an incorporation of engineered cystine to heavy chain or light chain of antibody, thus that enable the site-specific conjugation. The incorporation of unnatural amino acids into protein also used to facilitate site-specific conjugation via bi-functional linker. using this strategy, Herceptin and PE24 were conjugated site-specifically. The Herceptin-PE24 conjugate was does not affect their biochemical characterization such as antigen binding of antibody and catalytic activity of PE24. Also, its cytotoxicity was demonstrated for the HER2/neu-positive cells such as BT-474, SK-BR-3 and ZR-75-1 breast cancer cell lines, and showed comparable previous fused immunotoxin. We expect that the conjugation approach described in this study can be applied to prepare various antibody-protein conjugates.