This paper presents an isolated dual-input DC-DC converter with a PWM plus phase-shift control for fuel cell hybrid energy systems. The power switches are controlled by phase shifted PWM signals with a variable duty cycle, and thus the two input voltages as well as the output voltage can be regulated effectively. By using the second input capacitor and the high side switches as an inherent active clamping circuit, zerovoltage switching (ZVS) for the power MOSFETs on the primary side, and zero-current switching (ZCS) for the diodes on the secondary side are achieved respectively to improve the performance of the proposed PWM converter. The principle of operation is analyzed and some design considerations are discussed. Simulation results using PLECS are given to verify the proposed analysis and design. An experimental converter prototype has been designed, constructed and tested in the laboratory to verify the validity of the theoretical analysis and also demonstrate the converter’s performance over wide variations in input voltage.