Most of what is now Split's historic center was once the palace of Roman emperor Diocletian, surrounded by thick stone walls. What is now the Church of St. Martin was then a passageway for the walls' guards. His rule lasted from 284 to 305, and was partly known for the Diocleniatic Persecution, an official and bloody attempt to remove Christianity from the Empire (before Emperor Constantine made it the preferred religion in 324, a little over a decade after Diocletian's death).

As the only emperor to have voluntarily abdicated (due to ill health), Diocletian had the opportunity to plan for his retirement, and the palace in Split was built for this purpose. Diocletian did indeed retire to this palace until his death in 311. Like most emperors, he had come from the military, so the palace mixed pleasure with defense, and incorporated barracks and quarters within its notable walls.

While the Church of Saint Martin is thought to have been built in the fifth and sixth centuries, it still represents some of the history of Christianity in the Roman sphere of influence. Built within the palace of one of its most staunch persecutors, adapted from an existing surreptitious location, it would seem to have been intended for secret worship, although it came to be in a time when Christianity already had a firm cultural foothold in the region.

The oldest original element remaining within the church, which is only 1.6 meters wide and 10 meters long, is a Romanesque chancel screen from the 11th century. The rest of the interior has had to be rebuilt throughout the centuries. A Dominican convent has stood next to the church from the 14th century, and this order now oversees its use and maintenance.