Fibroin is a dominant silk protein that possesses ideal properties as a biomaterial for drug delivery. Recently, the development of fibroin nanoparticles (FNPs) for various biomedical applications has been extensively studied. Due to their versatility and chemical modifiability, FNPs can encapsulate different types of therapeutic compounds, including small and big molecules, proteins, enzymes, vaccines, and genetic materials. Moreover, FNPs are able to be administered both parenterally and non-parenterally. This review summaries basic information on the silk and fibroin origin and characteristics, followed by the up-to-date data on the FNPs preparation and characterization methods. In addition, their medical applications as a drug delivery system are in-depth explored based on several administrative routes of parenteral, oral, transdermal, ocular, orthopedic, and respiratory. Finally, the challenges and suggested solutions, as well as the future outlooks of these systems are discussed.