In a fuel cell system, a reformer supplies reformate to a fuel cell stack. A portion of the reformate flow is diverted for analysis by a hydrocarbon analysis system. Residual hydrocarbons in the reformate may damage the anodes of the fuel cell stack. Although incompletely-reformed reformate may include a variety of hydrocarbon compounds, the invention simply measures methane as an indicator of the overall performance level of the reformer. A currently preferred embodiment includes a catalytic combustion methane sensor. Combustion air and reformate are delivered in a fixed ratio to the sensor via positive displacement pumps. The system can provide alarm means or optionally a shut-off means to protect a fuel cell stack from elevated levels of hydrocarbons in the reformate stream.