This work demonstrates the UV nanoimprinting lithography (UV-NIL) of high refractive index and highly transparent polythioethers based on thiol-ene click chemistry. Herein, 9,9-bis(3-mercaptopropylphenylether)fluorene (BMPF) is designed as a new thiol monomer with a high refractive index, high transparency, and good processability for UV-NIL. Colorless polythioethers are synthesized from BMPF and ene monomers under mild thiol-ene click reaction conditions. Excellent transmittance (96%) of 400 nm light is observed in all the polymer films and high refractive index values of 1.5972-1.6382 are attained. UV-NIL using thiol-ene photopolymerization affords polymer nanoimprinting patterns with various features on the order of 100-500 nm without any fractures. To the best of our knowledge, this is the first report on UV-NIL of high refractive index and highly transparent polymers. Through proper monomer and polymer design, novel polythioethers with suitable glass transition temperature (T-g) values are developed with high refractive index, high transparency, and good UV-NIL processability. Furthermore, UV-NIL based on thiol-ene click chemistry is accomplished at the nanoscale. (c) 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2018, 56, 2175-2182