The  University of Applied Sciences in Elbląg is the first independent higher education institution in the post-war history of the city, but the history of higher education in Elbląg goes back to 1954, when Technical University of Gdańsk opened in Elbląg its Consultation Office, which was transformed into the Elbląg Branch of Gdańsk Polytechnic in 1969.

In 1991, in cooperation with Gdańsk University, a Teacher Training College and Foreign Languages Teacher Training College were founded, offering B.A. courses. These three institutions constituted the basis for founding the State Higher School of Vocational Education in Elbląg in 1998 (later changing its name to the University of Applied Sciences in Elbląg). It was established on the basis of Higher Schools of Vocational Education Act from the 26th of June 1997 and ministerial regulation from the 16th of June 1998.

The first Rector, prof. Zbigniew Walczyk, was nominated for one year by the Minister of Education and later elected twice for 4-year terms (1999-2003 and 2003-2007) by the Senate. Prof. Halina Piekarek-Jankowska was elected for the term 2007-2011. Prof. Zbigniew Walczyk was elected again for the term 2011-2015 and once more for the term 2015-2020. Prof. Jarosław Niedojadło was elected for the term 2020-2024.