In recent years, silk fibroin nanoparticles (SFNs) have been consolidated as drug delivery systems (DDSs) with multiple applications in personalized medicine. The design of a simple, inexpensive, and scalable preparation method is an objective pursued by many research groups. When the objective is to produce nanoparticles suitable for biomedical uses, their sterility is essential. To achieve sufficient control of all the crucial stages in the process and knowledge of their implications for the final characteristics of the nanoparticles, the present work focused on the final stage of sterilization. In this work, the sterilization of SFNs was studied by comparing the effect of different available treatments on the characteristics of the nanoparticles. Two different sterilization methods, gamma irradiation and autoclaving, were tested, and optimal conditions were identified to achieve the sterilization of SFNs by gamma irradiation. The minimum irradiation dose to achieve sterilization of the nanoparticle suspension without changes in the nanoparticle size, polydispersity, or Z-potential was determined to be 5 kiloGrays (kGy). These simple and safe methods were successfully implemented for the sterilization of SFNs in aqueous suspension and facilitate the application of these nanoparticles in medicine.