Chemistry has been a part of the University from its beginning. Initially, it belonged to the Faculty of Mathematics and Natural Sciences, and was organized by Antoni Basiński who came to Toruń in 1945 from Stefan Batory University in Vilnius. Since 1951, five Chairs directed by Antoni Basiński (Physical Chemistry), Witold Zacharewicz (Organic Chemistry), Ernest Pischinger (Chemical Technology), Antoni Swinarski (Inorganic Chemistry), and Alina Ulińska (General Chemistry), were established within the Faculty of Mathematics, Physics and Chemistry.

The scientific works started in 1948 when the construction of a new building, Collegium Chemicum, was completed. The areas of interest activity were colloids, polymers, inorganic chemistry, terpenes, and soda technology. In 1969 the Chairs were integrated into the Institute of Chemistry directed by Antoni Swinarski, who was later succeeded by Lucjan Borowiecki (1975-89) and Marek Zaidlewicz (1989-93). In 1973 the Institute was relocated to the present buildings at the University campus. Over the years, the number of faculty members has increased, and new research directions such as adsorption and catalysis, chemistry of organoboron compounds, zeolites, coordination compounds, polymer membranes, environmental and theoretical chemistry were included.

In 1993, the Faculty of Mathematics, Physics and Chemistry was divided and the Faculty of Chemistry was established. Marek Zaidlewicz was the first dean of the Faculty (1993-1999).