A membrane electrode assembly includes a proton exchange membrane, a first electrode and a second electrode. The proton exchange membrane has two opposite surfaces, a first surface and a second surface. The first electrode is located adjacent to the first surface of the proton exchange membrane, and the first electrode includes a first diffusion layer and a first catalyst layer. The second electrode is located adjacent to the second surface of the proton exchange membrane, and the second electrode includes a second diffusion layer and a second catalyst layer. At least one of the first diffusion layer and the second diffusion layer includes a carbon nanotube structure. A fuel cell using the membrane electrode assembly is also provided.