Local delivery of drugs and biopharmaceuticals for the treatment of inflammatory bowel disease remains a challenge. Innovative nanomedicines with appropriate properties raise the possibility of efficient drug targeting. Hence, the overall aim of this study was to develop and characterize a protamine-based nanosystem for topical delivery of therapeutics to inflamed intestinal mucosa following oral administration. Protamine nanocapsules with a new composition were for the first time prepared by, a self-emulsifying process, without the use of organic solvents or heat. A model lipophilic anti-inflammatory agent, cyclosporin A (CsA), was encapsulated in the oily core of these nanocarriers. The CsA-loaded formulation was isolated from the free drug by gel filtration and the entrapment efficiency was determined using reverse phase high-performance liquid chromatography (HPLC). Protamine nanocapsules had sizes within the range of 160-180 nm, with low polydispersity index (0.2) and positive surface charge, together with high entrapment efficiency (95%) and drug loading capacity (5%). The nanocapsules exhibited good stability in storage both as an aqueous suspension and as a freeze-dried powder. Nanocapsules also preserved their colloidal stability in simulated intestinal media. In vitro studies performed with the Jurkat human T lymphocyte cell line showed that CsA-loaded protamine nanocapsules are more efficient than the commercial Sandimmune Neoral® formulation at reducing IL-2 secretion (γγp<0.01). At the same time, nanocapsules showed no toxic effects on the cells. The results discussed herein indicate the feasibility of the developed nanosystem to serve as a potential carrier for cyclosporin A administration.