The gas diffusion layer (GDL) is an important component of the membrane electrode assembly of fuel cells (FCs). Its roles include supporting the catalyst layer, collecting current, and transferring and redistributing materials. A conventional GDL consists of a backing layer, typically of commercial carbon paper or carbon cloth, but it suffers from its high cost, narrow pore-size distribution, lack of flexibility and poor conductivity, and a micro-porous layer (MPL) is necessary for better gas/liquid management. A novel flexible gas diffusion layer (GDL) was prepared by vacuum filtration of a suspension of carbon fibers (CFs) and highly-dispersed multi-wall carbon nanotubes (MWCNTs) in a polytetrafluoroethylene (PTFE) binder and water repellent. SEM observations, gas permeability and porosity tests indicate that there is a gradient in the concentration of highly-conductive MWCNTs in the CNT-CF GDL network that facilitates electron transport. A multi-level pore structure is formed, which is beneficial to mass transport. The PTFE is distributed uniformly, which is favorable for the discharge of condensed water from the FCs. When the GDL/CNT-CF is used in the cathode, or in both the cathode and anode in direct methanol FCs, the maximum power densities of single cells are increased by 20% and 35%, respectively, compared with those using a commercial GDL consisting of carbon paper with a MPL due to its excellent mass transfer performance.