Breast cancer is the most common diagnosed cancer, and the second cause of cancer death among women, worldwide. HER2 overexpression occurred in approximately 15% to 20% of breast cancers. Invasive biopsy method has been used for detection of HER2 overexpression. HER2‐targeted imaging via an appropriate radionuclide is a promising method for sensitive and accurate identification of HER2+ primary and metastatic lesions. 99mTc‐anti‐HER2 scFv can specifically target malignancies and be used for diagnosis of the cancer type and metastasis as well as treatment of breast cancer. We radiolabeled anti‐HER2 scFv that was expressed in Escherichia coli and purified through Ni‐NTA resin under native condition with 99mTc‐tricarbonyl formed from boranocarbonate. HER2‐based ELISA, BCA, TLC, and HPLC were used in this study. In the current study, anti‐HER2 scFv was lyophilized before radiolabeling. It was found that freeze‐drying did not change the binding activity of anti‐HER2 scFv to HER2. Results demonstrated direct anti‐HER2 scFv radiolabeling by 99mTc‐tricarbonyl to hexahistidine sequence (His‐tag) without any changes in biological activity and radiochemical purity of around 98%. Stability analysis revealed that 99mTc‐anti‐HER2 scFv is stable for at least 24 h in PBS buffer, normal saline, human plasma proteins, and histidine solution.