The Department of Molecular Science and Engineering traces its origins to the Department of Applied Chemistry, established in 1917. In 1953, the Taiwan Provincial Taipei Institute of Technology set up a three-year Department of Textile Engineering, with textile engineering and textile chemistry groups. It was renamed the Department of Fiber Engineering in 1971 and reorganized as the Department of Textile Industry in 1979.

In 1994, the school became the National Taipei Institute of Technology and the department was upgraded to a four-year Department of Textile Engineering. The Master’s Program of the Institute of Organic and Polymeric Materials was established in 1998. In 2002, the department was renamed the Department of Molecular Science and Engineering, and in 2007 the Ph.D. Program of the Institute of Organic and Polymeric Materials was established.