The Academy of Fine Arts was founded in 1818 and originally functioned as the School of Drawing and Painting within the Literature Division of the Faculty of Philosophy of Jagiellonian University. Its originators were the Kraków painters Józef Brodowski and Józef Peszka, professors of drawing and painting. In 1833, the school, separated from Jagiellonian University, lost its academic character and functioned as the School of Drawing and Painting within the Technical Institute until 1873.

After becoming independent in 1873, it took the name of the School of Fine Arts, with Jan Matejko as its director. Thanks to his efforts, the academy, which was divided into drawing, painting, composition and sculpture departments, was moved in 1880 to its present building on Matejko Square.  In 1895, Julian Fałat became director, and in 1900, the school was renamed the Academy of Fine Arts and elevated to the status of a university.. Prominent artists of Young Poland lectured there: Jacek Malczewski, Leon Wyczółkowski, Jan Stanisławski, Teodor Axentowicz, Stanisław Wyspiański, Józef Mehoffer, Wojciech Weiss, Józef Pankiewicz, and Konstanty Laszczka. Thanks to Julian Fałat, the Academy became an important centre of European modernism.

During the First World War, the Austrians occupied the building for military purposes but did not close the university. In 1918, the Academy celebrated its centenary, and the eminent Professor Xawery Dunikowski joined the sculpture department.  Architecture and conservation of monuments were added to the subjects taught, which the Rector Adolf Szyszko-Bohusz took particular care of.  The collegemerged with the National Higher School of Visual Arts in 1950. The making of the curriculum into distinct faculties, which is still valid today, was introduced, and the buildings handed over to the Academy at that time continue to serve as the core of the Academy. In 1979, the Academy of Fine Arts was named after Jan Matejko.

The university's main building, designed by Maciej Moraczewski, was built between 1878 and 1879. It is a monumental edifice with a neo-Renaissance brick façade with large framed windows. Above the main portal is a framed window with the coat of arms of Kraków and a bust of Jan Matejko.

The Academy of Fine Arts continues to develop, but remains true to tradition yet open totoday's challenges. Currently, training is provided in the faculties of painting, sculpture, printmaking, interior design, art conservation and restoration, industrial forms and intermedia.

The main building houses the Museum of the Academy of Fine Arts, which collects and develops museum collections produced and collected by the Academy. The Museum was established between 2002 and 2003 based on historical collections collected since 1818. Today, it has more than 5,000 objects representing painting, drawing, sculpture, artistic textiles, and applied and design art.