Background Fluorescent imaging agents are becoming evermore important in preclinical and clinical research. They do, however, suffer from poor tissue penetration, which makes optical fluorescence imaging incompatible with whole-body imaging techniques. The design of novel bimodal PET active and fluorescent tracers could therefore combine the benefits of optical imaging with radioactively labeled imaging probes. Herein, we report the synthesis and evaluation of a clickable 18F-labeled fluorescent dye. Methods An azide-modified BODIPY-Fl dye could be successfully radio-labeled with 18F using an 18F/19F exchange reaction of the boron-fluoride core of the BODIPY dye to yield a clickable bimodal PET/fluorescent imaging tool. In vitro as well as in vivo imaging (PET/fluorescence) using a bombesin analog was conducted to study the applicability of the dual-modality imaging probe. Results We use the radio-labeled small molecule, 18F-BODIPY-azide to label site-specifically different targeted peptides, based on a standard modular labeling protocol. Following the synthesis of a bimodal bombesin analog, we determine the peptide tracer’s performance in vitro and in vivo, exploring both the optical as well as PET imaging capabilities. Conclusion This versatile methodology has the potential to have a transformational impact on 18F radiotracer synthesis, opening the door for rapid screening of novel-labeled peptide tracers, both on the cellular (optical) as well as whole-body (PET) level. Electronic supplementary material The online version of this article (doi:10.1186/s13550-015-0120-4) contains supplementary material, which is available to authorized users.