This paper reports on an experimental evaluation of the hydrogen separation performance in a proton exchange membrane system with Pt-Co/C as the anode electrocatalyst. The recovery of hydrogen from H2/CO2, H2/CH4, and H2/NH3 gas mixtures were determined in the temperature range of 100–160 °C. The effects of both the impurity concentration and cell temperature on the separation performance of the cell and membrane were further examined. The electrochemical properties and performance of the cell were determined by means of polarization curves, limiting current density, open-circuit voltage, hydrogen permeability, hydrogen selectivity, hydrogen purity, and cell efficiencies (current, voltage, and power efficiencies) as performance parameters. High purity hydrogen (>99.9%) was obtained from a low purity feed (20% H2) after hydrogen was separated from H2/CH4 mixtures. Hydrogen purities of 98–99.5% and 96–99.5% were achieved for 10% and 50% CO2 in the feed, respectively. Moreover, the use of proton exchange membranes for electrochemical hydrogen separation was unsuccessful in separating hydrogen-rich streams containing NH3; the membrane underwent irreversible damage.