Since 1^st century AD, Stobi occupied 27 hectares, framed by the fortification walls. The wall on the eastern side is around 450 meters long and only ten meters away from the river Crna. A small part of it was documented during the excavation of Casa Romana in 1972. The defensive wall is separated by an alley from Casa Romana. The eastern city wall was functional until the 4^th century when the town was flooded. The successive flooding was probably the main reason that a new wall was built at the end of the 4^th century or the beginning of the 5^th. It was constructed to the west from the previous and its foundations were put on top of some older buildings, such is the case of the “Building with Arches”. Theater seats were built in the defensive wall which chronologically determined its construction. The southeast part of the defensive wall was uncovered in 2008. It is preserved 4 meters above the foundations and there were couple of lines made of tiles above which the layers of stone continued. The corner where the old and the new wall bonded was discovered in 2009. An inner tower was built at that place. The line of the fortification wall on the southern, western and northern side remained the same during the centuries. There are many obvious repairs and even doubling of some parts. The average width of the defensive wall is 2.50 meters and there are 14 rectangular towers visible at the moment.

The only gate, discovered so far, is located at the southern segment of the fortification. This place was known as “Porta” among the local population long before the first excavations in 1930. In 1970 and 2001 – 2002 the gate was subject of research once again. The popular names of the gate, given by the archaeologists, are “Porta Heraclea” and “Porta Sacra”. The first one is due to the road which leads from the gate to the town of Heraclea Lyncestis while the second is linked to the fact that this is the only passage to the city cemetery.  The gate was indrawn from the line of the wall and there was an arched ante- gate in front of it. At the end of the 4^th or the beginning of the 5^th century, two towers were added at a distance of 9 meters from the gate. Seats of the theater were built in the towers. According to some scholars these towers mark the gate as a dypilon while others think they were propilon, as part of the proteichisma.

During the excavation in 2010, a new gate was discovered in the southeastern part of the fortification wall (in the sector Temple). The gate was closed in the 6th century.  

In 2009, there were 326 meters discovered from the western line of the fortification and two phases of its construction were recorded. The excavations in 2010 revealed that there were older buildings below the fortification wall. During the Late Antiquity the outside area close to the wall was used as cemetery.