Previously published work on fast charging method has demonstrated that the side reaction can be minimized by a properly designed charging protocol, but does not consider effect of lithium plating and stripping. Therefore, a model for side reaction, lithium plating, and stripping is developed and incorporated into a reduced order electrochemical model (ROM) with extended Kalman filter. In addition, effects of negative pulse charging are analyzed and show that negative pulse charging can recover ions from metallic lithium, so the capacity loss is minimized compared with CC charging with the same charging speed. Finally, a new fast charging method is designed by combining negative pulse and different limitations that include anode potential, side reaction rate and cutoff voltage that are estimated from ROM, which is called a fast charging method with negative pulse (FCNP). The proposed method, 2C and 3C CC/CV charging methods are tested in Battery-In-The-Loop using a large format pouch type lithium ion battery. The charging time by FCNP up to 80% SOC is comparable to that by 3C CC/CV at the beginning of life and faster after the middle of life. At the same time, the capacity loss by FCNP is comparable to that by 2C CC/CV.