Protein nanoparticles, as inherently biocompatible,programmable and engineerable carriers, possess great potential for targeted drug delivery, controlled release, and the simultaneous integration of diagnosis and therapy (theranostics). This review introduces the main types of protein nanoparticles, their sources, fabrication methods and stabilization strategies, and highlights their therapeutic, imaging, and theranostic applications, along with the design of next-generation protein-based nanovaccine featuring multivalent, particulate antigen display. The fabrication approaches encompass a wide range of techniques, from classical methods such as desolvation, emulsification, self-assembly, and thermal gelation to advanced strategies including nanospray, electrospray, and Nab technology. Stabilization is achieved through two main routes: covalent crosslinking and physical interactions. The protein sources include animal-derived proteins such as albumin and gelatin, as well as plant-based proteins such as zein. In terms of applications, these nanoparticles have been explored for passive targeting based on the enhanced permeability and retention (EPR) effect and active targeting via specific ligand–receptor interactions and intrinsic gp60/SPARC pathways. They have also been investigated for bioimaging, theranostic systems, and the design of novel protein-based nanovaccine platforms. Evidence indicates that these biocarriers outperform soluble formulations and synthetic carriers in enhancing therapeutic efficacy and reducing systemic toxicity, although challenges such as scalability and production uniformity still persist. Finally, emerging research directions and clinical translation opportunities are highlighted, outlining a promising outlook for the development of personalized therapies and next-generation vaccine designs.