Portable fuel cells are receiving great attention today mainly because their energy density is higher than any portable battery solution. Among other types, portable polymer electrolyte membrane (PEM) fuel cells are an established technology where research on increasing their efficiency is leading product development and manufacturing. The objective of this work was to study and evaluate the redesign of a commercial portable fuel cell, improving its efficiency. A three-dimensional model of the original PEM fuel cell with parallel plus a transversal flow channel design was developed using Comsol Multiphysics, including the effects of liquid water formation and electric current production. Using this model, the effects of different channel geometries and respective cathode flow rates on the cell’s performance, including the local transport characteristics, were studied. Laboratory tests with various fuel cell stacks using the new channels structure were effectuated for an evaluation of the fuel cell’s performance, showing improvements in its efficiency of up to 26.4%.