© 2019 John Wiley & Sons, Ltd. Labeling agents with radioisotopes or fluorescent dyes are useful for investigating the biodistributions of biologically active proteins and peptides. Compared with molecular imaging with a single modality, dual imaging probes provide complementary information for each modality. The development of a dual radioisotope/fluorescence agent for protein labeling would thus be valuable for both preclinical and clinical applications. In this study, we designed and synthesized a radioiodinated BODIPY derivative (BODIPY-ML) with a maleimide group as a thiol-labeling agent. In the presence of N-chlorosuccinimide and 1% acetic acid, [125I]BODIPY-ML was successfully obtained at a radiochemical yield of 42%. In conjugation studies, model proteins including RGD peptides and anti-HER2 VHH were successfully labeled with BODIPY-ML via covalent bonds. The results demonstrated the feasibility of the radioiodinated BODIPY as a dual-labeling agent via thiol groups.