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Functionalized carbon nanotubes (CNTs)/Nafion® nanocomposite membranes prepared by a surfactant-assisted method have been presented for fuel cell applications. 1 wt.% sulfonated CNTs (s-CNTs) and 1 wt.% oxidized CNTs (ox-CNTs) were reinforced into Nafion® membrane by adding 0.3 wt.% surfactant such as Cetyltrimethylammonium bromide (CTDMA), sodium dodecylbenzenesulfonate (SDBS), sodium 4-octylbenzoylsulfonate (SOBS) and hexadecyltrimethylammonium (HDTMA) in a solution casting procedure. The prepared s-CNTs or ox-CNTs reinforced Nafion® nanocomposites produced lower methanol uptake values than that of cast Nafion® while ion exchange capacity was maintained. Furthermore thermal property of the nanocomposites was enhanced.