The basilica was built in the early 5th century AD, during the Early Christian period, when Cyprus was part of the Byzantine Empire. It originally comprised three aisles with two rows of marble columns, an apse and a narthex. The floors and walls were decorated with coloured mosaics in geometric patterns.
In 653, it was almost destroyed during the Arab raids against the island. The Arabs maintained a garrison, using the structure as workshops, stables and living quarters for the army. They also built a tower in its narthex which could have served as a watchtower, lighthouse or a minaret. In 688, after they evacuated the island, the church was restored as a three-aisled barrel vaulted basilica in a smaller scale than the previous one.
In 1159, the basilica was destroyed again. This time, according to Neophytos of Cyprus, an earthquake destroyed the church as well as thirteen churches in the district of Paphos.
In the following years, a smaller structure was built upon the ruins of the basilica but it was destroyed by the 1222 earthquake.
The church was left in ruins and forgotten.
The exact location of the basilica was unknown among the other ruins of Nea Paphos ("New Paphos") until the 20th century. The Panagia Limeniotissa was first discovered in 1937 and was officially excavated in 1959. Today, the Panagia Limeniotissa basilica is part of Paphos Archaeological Park which is a UNESCO World Heritage Site.