In this work, a mathematic model is developed to describe an experimental methane fuel processor which is intended to provide hydrogen for a fuel cell system for power generation (2-3KW). Experimental work was carried in the facilities of Union Chemical Laboratory (UCL) of Industrial Technology Research Institute (ITRI) (Lee et al., 2002). First principle reactor models were constructed to describe a series of reactions, reforming (SR/ATR), high & low temperatures water gas shift (HTS /LTS), preferential oxidation (PROX) reactions, at different sectors of the reactor system for autothermal reforming of methane as well as gas cleaning (Choi and Stenger, 2003; Choi and Stenger, 2004; Pacheco et al., 2003). The pre-exponential factors of the rate constants were adjusted to fit the experimental data and the resultant reactor model provides reasonable good description of both steady state and dynamic behavior. Next, sensitivity analyses were performed to locate the optimal operating point of the fuel processor, the objective function of the optimization is the efficiency of the fuel processor (Lattner et al., 2004; Pacheco et al, 2003). Dominate optimization variables include: the ratios of water and oxygen to the hydrocarbon feed to the ATR reactor, and ATR reactor inlet temperature. The results indicate that an additional 2.5% improvement in the fuel processor efficiency can be made as compared to the present operation condition. Finally, the control issue is addressed. The control objective of a fuel processing system is quite clear: provide responsiveness to the changes in hydrogen demand while keeping the carbon monoxide concentration below 100 ppm. Two control structures are proposed. One uses the fuel feed flow rate as the throughput manipulator (TPM) and the other use the reactor outlet flow as the TPM. In both control structures, we can maintain the CO at allowable level, and we get faster dynamic response in the control structure with reactor outlet flow as the TPM.