The first exhibition of the Bocskai Museum was opened in 1958 on the initiative of an enthusiastic history teacher in the local secondary school, Dr. Imre Juhász.
From 1957 he and a group of students in his history club collected the first objects for the museum. The collection soon grew into a movement across town. The newly opened museum was named after István Bocskai, Prince of Transylvania, who settled the Haiducks in Hajdúszoboszló.
The museum got its licence in 1964 and was accepted as a member in the Hajdú-Bihar County Directorate of Museums. It was delegated the task of collecting objects from Hajdúszoboszló and its vicinity. Under the management of Dr. Imre Juhász (1964-2005), the Bocskai Museum became a significant and popular museum in the region.
In 2013 the maintenance of the museum was taken over by the local government of Hajdúszoboszló.
From 2014 Dr. László Bihari-Horváth is the curator of the museum, which is today a dynamically developing institution.