In the present work, gas–liquid two-phase flow behavior in minichannels bounded with permeable walls under flow conditions relevant to fuel cell applications was investigated. Two-phase flow pressure drop was measured and the data showed significant deviation from the Lockhardt–Martinelli (LM) approach due to the unique liquid side-introduction in the present work. A new approach was then developed to improve the prediction of two-phase pressure drop by incorporating variations of the liquid velocity along the channels into the original LM approach, which can be potentially employed to predict pressure drops in Proton Exchange Membrane Fuel Cells (PEMFCs) where liquid water emerges into the gas channels from the gas diffusion layer. Liquid slugs were found to occur in the channel section bounded with a permeable wall at high liquid flow rates and low gas flow rates, as well as in the extended channel. An attempt was also made to develop a criterion for predicting the onset of slugging based on the instability analysis of stratified flow in minichannels. The theoretical prediction gave reasonable agreement with the experimental data on the onset of slugging flow in minichannels. However, an advanced approach is still needed in the future to predict the initiation of slugging since it is a critical issue in water management for PEM fuel cells.