This is the most significant Christian building in Stobi. It is located to the west from the theatre and we can follow its existence in two separate periods. The basilica was excavated for the first time in 1918 and since then there were campaigns in 1924 – 25, 1927, 1934, 1970 – 78, during the `80s and during the `90s.
The first period is related to the Old Episcopal Basilica, built in the first half or the middle of the 4th century, which makes it the oldest church in R. Macedonia. It is possible that the basilica was built by the bishop Budius who took part in the first ecumenical council in Nicaea in 325 AD. It has a three aisled concept in which the central aisle is divided from the side ones by a colonnade. In the second half of the 4th century the basilica was expanded towards east. The south and the north wall were reconstructed. The floor was decorated by a mosaic divided in three zones. There is a section on the mosaic with an inscription mentioning the bishop Eusthatius as the commissioner of the reconstruction. The preservation of the frescoes from the 4th century, on the south and north wall, is a unique situation in Macedonia. They depict geometrical ornaments, animals and saints.
The second period begins with the construction of the new monumental basilica in the first half of the 5th century. The inscription which once stood over the main entrance of the nave reveals the name of Bishop Philip as the builder of the church. It is interesting that the construction activities did not destroy the remains of the old basilica. Huge 4 m foundations were built and the inside space was covered. This allowed the Episcopal Basilica to dominate the surrounding area. The two storey building incorporated many seats and columns from the theatre which emphasizes its grandeur.
The atrium of the basilica was entered from the street of Via Sacra. The next room is the narthex, divided in three zones by two pairs of columns. The walls were decorated with frescoes and the mosaic floor depicts animals and geometrical motifs. The nave and the accompanying rooms were entered from the narthex. The steps on the south side lead to the baptistery.
The central aisle was separated from the north and the south one by a colonnade. The columns were founded on a stylobate made of seats from the theatre. The floor was made of marble tiles combined with segments of mosaic and sandstone slabs. In the eastern half there were the ambo and the altar. The marble plates from the altar screen were decorated with reliefs of crosses. The floor and the altar were reconstructed. At the eastern end there is a double apse. A crypt is located in the inner apse and the outer one had a window with massive impost capitals. Some of the capitals were painted and gilded.
The southern and the eastern aisle had fresco decorated walls. The southern aisle was reconstructed and it has two mosaic floors one above the other. The older floor was cut with the foundation of a tomb. The deceased might have been one of the bishops. The south wall of this aisle was doubled and there is another tomb inside.
The baptistery is to the south of the basilica and its northern wall is attached to the new wall of the southern aisle. It has the plan of an inscribed quatrefoil and it was covered by a dome. There is a piscina in the center with steps on two sides. The mosaic floor is decorated with peacocks flanking a kantharos and deer flanking a kantharos. This is allusion of Psalm 42. The walls had frescos with figures of saints. From the beginning of the 6th century a marble kantharos was added on top of the piscina.
According to a coin discovered below the ruins of the walls it can be concluded that the basilica was destroyed years after 569 – 70 AD.