The exhibition is arranged in chronological order, in three rooms: Room A (vestibule) contains finds of the prehistoric period. Of the most important exhibits are the Neolithic figurines and tools from the settlement at Kolchis (case 1, upper and lower shelf).

Case 2 contains a small collection of fine bronze jewellery dated to the Early Iron Age, from various sites of the Kilkis region. It includes mostly bracelets with many spirals, rings and pendants, the latter presenting a variety of types and shapes, such as anchors, pyxides, birds and vases (upper and lower shelf).

Due to the restricted space of the Museum, in the same room are also exhibited a funerary stele with a relief representation of a rider, part of an Attic sarcophagus with a representation of young men and a horse, and a honorary decree of the city of Morrylos (Ano Apostoloi).

Room B contains excavation finds from the Iron Age cemetery at Old Gynaikokastro, including characteristic urns and grave offerings, weapons, knives, double axes, and jewellery. Reproductions of burials are displayed at the corners of the same room.

Finds of the historic periods, mostly sculpture, vases, jewellery, and objects of everyday life are displayed in Room C. Among the most impressive exhibits are: the kouros of Europos, dated to the end of the 6th century B.C., four statues from the Heroon of Palatiano, dated to the 2nd century A.D., a statue of Dionysos, also from Palatiano, and two statues of Apollo and Aphrodite, from Mikro Dasos and Chorygio, respectively.

Items given by individuals or found during old excavations are exhibited in cases 6 and 7. The centre of Case 6 is occupied by a well preserved Classical helmet with an incised scene of facing lions on the front, while the rest of the items are vases and figurines from various sites.

Case 7 (upper shelf), includes clay, gilt plaques with representations of griffins devouring stags, and many other items, all grave offerings found at Philyria.

Finds from the excavations of Palatiano, mostly objects of everyday life activities, are exhibited in case 8. Impressive among them are the bone spoons, the incised loom-weights, and the terracotta statuettes.