This work presents a fundamental theory and methods for understanding the gas composition dynamics in PEMFC anode fuel supply compartments operated dead-ended with recirculation. The methods are applied to measurement data obtained from a PEMFC system operated with a 1 kW short stack.We show how fuel utilisation and stack efficiency, two key factors determining how well a fuel supply system performs, are coupled through the anode gas composition.The developed methods allow determination of the anode fuel supply molar balance, giving access to the membrane crossover rates and the extent of recirculated gas exchanged to fresh fuel during a purge. A methane tracer gas is also evaluated for estimating fuel impurity enrichment ratios.The above theory and methods may be applied in modelling and experimental research activities related to defining hydrogen fuel quality standards, as well as for developing more efficient and robust PEMFC system operation strategies.