A new varying current decay (VCD) protocol, which charges the Li-ion battery at a faster rate, was developed. The performance of the battery charged using the VCD protocol was compared with the performance of batteries charged with conventional constant current–constant voltage (CC–CV) and constant voltage (CV) protocols. The destructive physical analysis tests at the end of 150 cycles indicated higher impedance for the cells cycled using the VCD protocol compared to the cell charged using the conventional (CC–CV) mode. The observed increase of the impedance was due to a small increase of the potential above the cut-off value of 4.2 for short times. A complete capacity fade material balance as a function of number of cycles was performed in order to account for the total capacity loss due to different charging protocols used. The loss of primary active material (Li+), the secondary active material (LiCoO2/carbon) and the rate capability losses were determined for Sony US 18650 Li-ion cells and compared for different charging protocols.