On May 25, 1925, the state authorities established a tertiary school, which was called the Higher School of Commerce (Wyższe Studium Handlowe, WSH). The first ceremonial inauguration of the academic year took place on October 1, 1925. This moment is considered to be the beginning of today's Cracow University of Economics.

The university offered three-year and, with time, four-year programs in several fields. The lecturers were mostly professors from the Jagiellonian University and the Mining Academy (today's AGH). Initially, the premises were located at 2 Kapucyńska street, but after a few years it managed to erect its own buildings on Sienkiewicz street.

On September 1, 1938, the WSH was included among the academic schools, receiving the name Commerce Academy (Akademia Handlowa, AH). Arnold Bolland, the founder of the WSH, was elected the first president of the new institution. The Academy still had the status of a private university and operated based on student tuition. After the Nazi invasion, the Commerce Academy was closed, and its professors - along with lecturers from the Jagiellonian University and the Mining Academy - were insidiously arrested and deported to a concentration camp. The buildings were seized by the Nazi occupation authorities and the furnishings were largely destroyed. A small number of students continued to attend classes and take exams thanks to the clandestine teaching of a number of professors who returned from the concentration camp.

After the liberation from Nazi occupation, the Commerce Academy resumed its activity, enjoying an influx of numerous candidates for studies. Initially, the pre-war program was reinstituted, and in 1945, graduates could be awarded the degree of Master of Science in Economic and Commercial Sciences. However, a private university did not fit into the new political reality and in 1950 during the intensive introduction of Soviet systems by the communist authorities, the Commerce Academy was nationalized. It was then called the Higher School of Economics (Wyższa Szkoła Ekonomiczna, WSE). It offered programs in three faculties: Industrial Planning, Trade, and Finance. In 1954 these became the faculties of Industry, Trade, and Merchandise Sciences. New curricula were introduced in line with Marxist ideology and focused on narrow industry-specific education. Some former professors were removed and new lecturers were hired, who often lacked adequate academic backgrounds, but were nonetheless granted the title of associate professor. In 1952, the seat of the University was moved to the building of the former Aleksander Lubomirski Foundation boys’ home at 27 Rakowicka street.

In 1956 political transformations took place (the so-called "Polish October") that, thanks to the restoration of greater freedoms, resulted in advancing the Higher School of Economics to a higher level of teaching and research. In 1958, the Faculty of General Economics was established in place of the Faculty of Industry. This new faculty had a view to a more in-depth and broader profile of studies. Awarding of the doctoral degree was restored in place of the title of “candidate of sciences”, which followed the Russian system.

In 1959, after stricter criteria were established for higher schools, the WSE was transformed into a one-faculty school called the Faculty of Production and Trade (Wydział Produkcji i Obrotu Towarowego, WPOT). This new incarnation offered three fields of study: general economy, trade, and merchandise sciences. In 1968, student demonstrations in defense of civil liberties enshrined in the Polish Constitution (the "March events") took place across the Polish academic community. Students at the WPOT took an active part in them. The state authorities responded with repressions against rebellious students and lecturers, and by unleashing a campaign of anti-Semitism. As part of this campaign, the school expelled Dr. Hab. Edward Łukawer, an economist who held a communist political orientation, but who chose not to hide his Jewish heritage. Throughout Poland, new restrictions were imposed on the freedom of academic activity and the independence of universities. Organizational changes in the WPOT consisted in the creation - in place of departments - of larger units (institutes), and the division of the University into two faculties: Economics of Production, and Economics of Trade.

Despite such challenges, the future University continued to develop: the number of students increased, new classroom buildings were brought into use, and IT equipment was introduced. In 1974, the name of WSE was changed to the Economics Academy(Akademia Ekonomiczna, AE), and in 1975, it celebrated the 50th anniversary of its establishment. At that time, references were made to the traditions of the university and employees of merit, by restoring the university colors and student caps, and by naming some of the classrooms after deceased professors, etc. The political events of 1980 had notable impact on the life of the Academy. The vast majority of employees supported the creation of the NSZZ "Solidarity" free trade union, AE students associated with the newly formed National Union of Students (NZS) joined the nationwide student strikes, and in the spring of 1981 representatives of the entire academic community held democratic elections to choose the Rector, his chancellery, and authorities of the various faculties. The imposition of martial law in December 1981 was peaceful at Academy (none of the employees were interned), and while further reforms were halted, some of the newly introduced academic freedoms were not revoked.

The political transformation in 1989 and the subsequent transition to a market economy opened up new challenges and opportunities for rapid development for the AE. New fields of study were launched, which enjoyed great popularity. The number of students grew rapidly and organizational changes took place. The AE statute that had been in force since 1992, restored Chairs (in place of Institutes) in a three-faculty structure of Faculty of Economics (Economics and International Relations since 2003), Faculty of Management, and Faculty of Merchandise Sciences (initially as an Institute with faculty rights). In 2002, the Finance Department was established as a fourth faculty. The building of the Main Library was completed, and two new didactic pavilions with sports facilities were erected.

At the request of the University Senate, the Sejm of the Republic of Poland, on July 6, 2007, passed an act giving the AE a new name: the Cracow University of Economics (CUE).

In July 2015, the CUE Senate reached a positive decision on the motion to establish the new Department of Economy and Public Administration. It has been operating since October 2016 as CUE’s fifth faculty.