Currently marketed drug eluting stents (DES) are mainly matrix based systems, with drug entrapped in a carrier system. However, biocompatibility and other issues are associated with these matrix carrier systems. An alternate approach is the use of carrier-free DES, yet preventing functionalities of the carrier. Considering this, the objective of the present contribution is to develop a novel surface crystallization procedure for rapamycin (RM) coating on metallic stent. The physicochemical principles of the crystallization and key process parameters were extensively studied for fabrication of controllable and homogeneous crystalline coatings on stent scaffolds. Stents loaded with nearly 100 μg RM were chosen as a potential therapeutic device with multilayer coating of thickness 3–5 μm. In vitro RM release from these coated stents showed constant RM release for over 90 days and stability studies proves stability of developed RM coating when exposed to different storage condition for 6 months. In conclusion, developed crystallization process was found effective for fabrication of DES with stable coating. This process has wide applications and can be further implemented for other drugs for effective local drug delivery from implantable medical devices.