The increase of charging current can reduce the charging time, however, this increased charging current accelerates the speed of degradation and heat generation. There have been many suggested classical charging methods that include constant current and constant voltage, pulse charging or a combination, but few of these charging methods have been designed by considering the fundamental mechanisms of ion transport, chemical reactions, and intercalation process. Therefore, in order to minimize degradation rate and reduce charging time simultaneously, a charging method was designed for the beginning of life of battery by considering different limiting factors such as surface ion concentrations, state of charge, cutoff voltage, and side reaction rate, which generates different charging protocols. The designed protocols were implemented in real time using the Battery-In-The-Loop (BIL) system. Experimental results have shown that the proposed charging methods can reduce about half of the charging time compared with 1C CC/CV normal charging method recommended by manufacturer. Fast charging protocol considering side reaction rate and ion concentration yields the best performance among others in that the charging time can be reduced more than 40% compared with the normal charging with a degradation rate comparable with that of the normal charging up to 100 cycles.