The water vapor transfer across a Nafion® membrane exhibits an undesired non-minimum phase behavior. This paper will show that even in the disturbance-to-output loop, the non-minimum phase zero adversely affects the feedback controller design because of the coupling effect between the disturbance-to-output and the input-to-output loops. The non-minimum phase zero location is influenced by the channel plate structure and the membrane material property. The structural parameters examined in this research include channel plate dimensions and heat transfer coefficients. The membrane properties studied include membrane vapor transfer properties described in the Arrhenius’ equation. A governing equation to link the non-minimum phase zero and the parameters is developed in this paper. This equation shows that the non-minimum phase zero arises from the competing heat and mass transfer dynamics, and is determined by the structural parameters and membrane properties. A sensitivity study is presented and shows that structural and material property optimization can be used with the control system design to mitigate the non-minimum phase behavior in the PEM fuel cell humidification system.