Boron dipyrromethene (BODIPY), as a traditional fluorescent dye, has drawn increasing attention because of its excellent photophysical properties like adjustable spectra and outstanding photostability. BODIPY dyes could be assembled into nanoparticles for cancer imaging and therapy via rational design. In this review, the bio‐applications of BODIPY‐containing nanoparticles are introduced in detail, such as cellular imaging, near‐infrared fluorescence imaging, computed tomography imaging, photoacoustic imaging, phototherapy, and theranostics. The construction strategies of BODIPY‐containing nanoparticles are emphasized so the review has three sections—self‐assembly of small molecules, chemical conjugation with hydrophilic compounds, and physical encapsulation. This review not only summarizes various and colorific bio‐applications of BODIPY‐containing nanoparticles, but also provides reasonable design methods of BODIPY‐containing nanoparticles for cancer theranostics. This article is categorized under: Diagnostic Tools > in vivo Nanodiagnostics and Imaging