Two rooms of the museum are dedicated to the period of the Middle Ages. The visitors have the chance to learn about the economic, social, political and cultural development of the Albanians, who have preserved their typical characteristics also with documents and facts that speak clearly about the Albanian resistance against the ruling of Byzantines, French, Turks and Serbs. The display cases show testimonies of the development of agriculture in Kosovo, Scutari, Lezhe, Elbasan, Korca, Delvina and especially in Muzeqe where wheat for exportation was produced. Also testimonies of the coinage of coins of the Albanian Principalities and the circulation of foreign coins like Byzantine, Venetian, Serbian and French. A special place is occupied by the exhibition of a high number of architectonic works of art and like the Castle of Berat, Scutari, Prizren, Durazzo. The age of Skenderbej is shown also through the collection of books in European language (approximately 1000 volumes in 21 languages), dedicated to “The athlete of Crsito, Gjergj Kastrioti Skënderbeu”.

An important place in this pavilion is occupied by a famous collection of icons by the notorius painter Onufri (16^th century) and by David Selenica (18^th century). In this pavilion objects are exhibited that were connected, in origin, to Albanian princes: coat of arms, the famous inscription of Arber of the 12^th century, the monumental Gate of the Monastery of Gjon Vladimirit in Elbasan, with the coat of arms of Prince Karl Topia of the 14^th century. Typical in its genre and representative of the creative spirit of the Albanians it is the Epitaph of Gllavenica dated 1373. This rare original work has the image of the Dead Christ in the centre with figures of angels and floral symbols, by the hand of the famous Albanian artist Gjergj Arianiti.

The French byzantine scholar: André Grabar has asserted that the Epitaph of Gllavenica is the second in its genre, in Europe, for the 19^th century. The presentation of the growth of the Albanian towns of the second half of the 18^th century, the creation of the two large pashallëqe: that of the Bushatllinjve in the North of Albania, with the center of Scutari, and in the South that of Ali Pashë Tepelena with the town of Janina.