A novel aqueous fluorine-containing polyurethane was prepared with a hydrophobic macromonomer of a perfluoroalkyl group. Two representative properties of the polyurethane, initial particle diameter dispersed in water and surface free energy of coating films, were investigated. The macromonomer was synthesized by radical copolymerization of perfluoroalkylethyl acrylate and methyl methacrylate with a diol of chain-transfer agent in order to attenuate solubility and hydrophobic property. Anionic aqueous polyurethane was obtained with a good hydrophobic film property by one-step condensation polymerization of the macromonomer with hydrophilic comonomers and successive ionization. The polyurethane showed an initial average diameter of less than 1100 nm in water and surface free energies of less than 19 dyn/cm. The water dispersion property and hydrophobic surface property of the polyurethane can be controlled by controlling the content and hydrophobic property of the macromonomer. The incorporation of the macromonomer in the polyurethane backbone did not show a significant effect on the glass transition temperature, or the softness, of the polyurethane.