Fuel cells directly convert chemical energy stored in fuels into electrical energy through electrochemical reactions and have been identified as one of the most promising technologies for the clean energy industry of the future. In recent years, fuel cells have been applied in the medical field in both exploratory research and prospective products, as they offer multiple advantages over conventional batteries, including ease of recharging, environmentally friendly character and high security. In this paper, we summarize the up to date progress of this energy system in implantable medical devices which use microorganisms, enzymes and precious metals as catalysts, respectively. Safety is the most concerned issue in this application. In addition, we introduce a variety of applications of fuel cells on the vitro medical equipments (such as blood glucose meter, alcohol tester, wound treatment instrument). The introduction of fuel cells on implementable medical devices is in early stage of research, nonetheless the prospects/potential of this application are grant. Evidently, mankind could come across a new medical revolution upon the successful introduction of fuel cells to the human body.