According to the cultural traces and nekropols, the history of Novalja begins in the neolith. In records, first time it is mentioned by Plinius and later by Konstantin porfirigenet in the 10th century. At first it was named Cissa- todays Caska and later Kissa, once the main settlement on the island, after which port it will get his name.

The city has a long and rich history of what are testifying the numerous remains of Roman buildings, specially the three early cristian basilicas from the 4th century. Remains of mosaics, from one of them, can be seen in the church of the Holy Mother of God from Ružarija in the center of the city. Numerous artifacts and parts of them are exhibited in the arheological collection Stomorica next to the church.

One of the biggest atraction in Novalja is the Roman underground aqueduct, built in the 1st century before Christ.