In molecular imaging research, the development of multimodal imaging probes has recently attracted much attention. In the present study, we prepared radioiodinated BODIPY and applied it as a nuclear and optical dual functional labeling agent for proteins and peptides. We designed and synthesized [125I]BODIPY with a N-hydroxysuccinimide (NHS) ester, and evaluated its utility as a nuclear and fluorescent dual labeling agent for proteins and peptides. In the radioiodination reaction of BODIPY-NHS with [125I]NaI, [125I]BODIPY-NHS was obtained at a 48% radiochemical yield. When we carried out the conjugation reaction of [125I]BODIPY-NHS with bovine serum albumin (BSA) and RGD (Arg-Gly-Asp) peptide as a model protein and peptide, respectively, [125I]BODIPY-BSA and [125I]BODIPY-RGD peptide were successfully prepared at 98 and 82% radiochemical yields, respectively. Furthermore, we prepared [123I]BODIPY-trastuzumab by this conjugation reaction and successfully applied it to single photon emission computed tomography (SPECT) imaging studies using tumor-bearing mice, suggesting that radioiodinated BODIPY-NHS serves as a dual functional labeling agent for proteins and peptides. Since iodine has various radioisotopes that can be used for SPECT and positron emission tomography (PET) imaging, biological research, and radiotherapy, the radioiodinated BODIPY may be extensively applicable from basic to clinical research.