Lithium ion (Li-ion) batteries have been widely used in various kinds of applications, including consumer electronics, green energy systems and electrical vehicles. Since the charging method has a significant influence on the performance and lifetime of Li-ion batteries, an intelligent charging algorithm which can properly determine the charging current is essential. In this study, a fuzzy-logic-control-based (FLC-based) five-stage Li-ion battery charger is proposed. The proposed charger takes the temperature rise and the gradient of temperature rise of battery into account, and adjusts the charging current accordingly. To further improve the performance of the proposed FLC, the fuzzy-based Taguchi method is utilized to determine the optimal output membership functions (MFs). Comparing with the conventional constant current-constant voltage (CC-CV) method, the charging time, charging efficiency, average temperature rise and the obtained cycle life of the Li-ion battery are improved by about 58.3%, 1.65%, 26.7% and 59.3%, respectively.