Polymer electrolyte membrane fuel cells (PEMFCs) have many good characteristics for small power sources such as low operating temperature and high power density. In this study, the effects of thermal management on the performance of PEMFC systems using natural gas fuel, and the effects of integrating PEMFC systems with turbomachines, were investigated. Firstly, performance of various system configurations differing in the thermal management of reforming and stack cooling processes was comparatively analyzed. Then, various integrated system combinations with turbomachines (compressors and turbines) were analyzed. We performed a parametric analysis of the influence of turbine inlet temperature and compressor pressure ratio on system performance, and a 10% difference in efficiency among four simple PEMFC systems was predicted. Pressurization of the PEMFC with adequate thermal management may improve system efficiency, while efficiency enhancement from corresponding simple PEMFC systems was hard to achieve in the ambient pressure integrated systems.