The growing market for clean, sustainable energy systems has opened to door for many technologies in both the power generation and transportation sectors. Fuel cell technology has provided a means to produce power and heat more efficiently and with fewer emissions than traditional power generation systems. The emergence of hydrogen fuel cell vehicles has demonstrated the use of fuel cells for transportation that use hydrogen fuel to achieve comparable performance to traditional vehicles while achieving greater efficiency and zero emissions. This thesis focuses on a system that brings the two sectors together by utilizing fuel cell technology to tri-generate three useful products from a renewable biogas stream: power, heat, and hydrogen. The hydrogen produced is then directly used at a fueling station to refuel hydrogen fuel cell vehicles. A fully operational system has successfully demonstrated this technology at the Orange County Sanitation District which provided the inspiration for this work. A dynamic tri-generation system has been modeled with investigation of electrochemical hydrogen separation to produce high purity hydrogen necessary for fuel cell vehicles. Results from this analysis show a wide range of design and operational values to characterize the performance under many conditions. Electrochemical separation has unique operation compared to other separation methods and can improve system performance especially in sub megawatt systems. It is shown that tri-generation systems have great promise as an energy system because of their efficient operation, near zero emissions, ability to run on renewable biogas, and the ability to produce the hydrogen fuel for fuel cell vehicles.