The College of Eastern Europe was established in 2001 by Jan Nowak-Jezioranski, who secured support from the City of Wrocław, the Lower Silesian Voivodeship, the Ossoliński National Institute, the Krzyżowa Foundation, and the Angelus Silesius Meeting House. The idea for the organization originated in Spring 2000 during a visit to Krzyżowa, with the core goal of fostering collaboration and promotion of democratic institutions between countries formerly comprising the Republic of Poland. The founding meeting took place on February 8, 2001, at Wrocław Town Hall. It was preceded by a Mass at Wrocław Cathedral celebrated by Cardinal Henryk Gulbinowicz, with the Foundation later being officially registered on May 19, 2001.
The College of Eastern Europe began under difficult circumstances; It had no headquarters, no budget, and no employees. However, it had a charismatic initiator in Jan Nowak-Jezioranski. Despite his almost 90 years of age at the time, he came to Wrocław regularly and was a critical force behind the organization in its early days, pushing forward through these constraints.
One of the first activities of the College was to organize the Festival of Ukrainian Culture, UKRAINA VIVA!, which was the first major presentation of Ukrainian culture in Wrocław. The festival was prepared by the newly-established foundation in cooperation with the Wrocław Center for Culture and the Arts. Ostap Protsyk, a young journalist and columnist from Lviv, became the artistic head of the festival. The next festival was the Festival of Belarusian Culture, which coincided with the signing of an agreement by the city of Wrocław to establish a partnership with the city of Grodno, Belarus, in 2005.
In January 2005 the initiator and founder of the College of Eastern Europe, Jan Nowak-Jezioranski, passed away after a long and serious illness. He was buried at Powązki Cemetery in Warsaw. After the passing of its founder, the College of Eastern Europe took his name, becoming known as the Jan Nowak-Jezioranski College of Eastern Europe in Wrocław.
An important moment in the history of the College of Eastern Europe was the establishment of two periodicals: the bimonthly Nowa Europa Wschodnia and the (initially quarterly, and now) bimonthly New Eastern Europe. Both magazines are based in Kraków.
In 2009–2011, the College of Eastern Europe coordinated the construction of the Memorial to the Murdered Professors of Lviv in Lviv, Ukraine.
Since 2014, the College of Eastern Europe has managed the Castle on the Water in Wojnowice, near Wrocław.
