This paper presents the analysis and design of a smart battery management system for Field Programmable Gate Array (FPGA) based portable electronic devices. It is a novel concept of incorporating the functionality of a smart battery management system into the FPGA used by portable electronic devices, which provides the following advantages. (1) It lowers cost since the conventional commercial independent battery management circuit can be eliminated; (2) It offers more flexibility because FPGA based battery management algorithms can be specifically designed for different battery chemistries of different devices and can provide the flexibility of algorithms and functionalities updating as well. Smart battery management system concepts include four aspects: (1) smart charging; (2) battery balancing; (3) smart discharging; and (4) safety operating. One novel charging algorithm, which combines the merits of multistage charging and pulse charging, is proposed to charge a Li-ion battery pack smartly. A Proportional Integral (PI) control method is introduced to achieve the current control of charging circuit with considerable close loop stability. Simulation results from the PSIM 9.0.4 software package and experimental results from the prototype built in the lab are demonstrated to verify the effectiveness of smart charging. The realizations of battery balancing, smart discharging, and safety operating are also briefly described by taking advantage of the proposed FPGA based smart battery management system topology, which verify the feasibility of the proposed FPGA based smart battery management system for portable electronic devices.