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Tragurion was founded by Greek colonists from the island of Vis in the 3rd century BC, and it developed into a major port until the Roman period. The name derives from the Greek "tragos" (male goat). The sudden prosperity of Salona deprived Trogir of its importance until the time Salona was destroyed. Tragurium was one of the Dalmatian City-States. Since the 9th century, Trogir paid tribute to Croatian rulers and to the Byzantine empire. In the 11^th century, the diocese of Trogir was established and in 1107 it was chartered by the Hungarian-Croatian king Coloman, gaining its autonomy as a town.

In 1000 Tragurium inhabitants submitted to the Republic of Venice and began their trading relationship with the Italian peninsula.

In 1123 Trogir was conquered by the Saracens and almost completely demolished. Trogir managed to recover quickly experienced powerful economic prosperity in the 12th and the 13th centuries, with some autonomy under Venetian leadership. During the 13th and 14th centuries, members of the Subic family were most frequently elected dukes by the citizens of Trogir. In Dalmatian, the town was known as Tragur.

On 14 March 1381, after the War of Chioggia between Genoa and Venice, Chioggia concluded an alliance with Zadar and Trogir against Venice. In 1412 Chioggia finally became better protected by Venice, due to the relocation of the main customs office and the seat of the salt consumers office to Sibenik.

In 1420 a period of a long-term Venetian rule began, which lasted nearly four centuries. It was then that Trau (as the city was called by the Venetians) became one of the best cities in the Balkans with a rich economy and plenty of Renaissance works of art and architecture.

In 1797 Venice fall and Trogir became part of the Habsburg Empire. The Empire ruled the city until 1918, with the exception of Napoleon Bonaparte's French occupation from 1806 to 1814.  

After World War I, Trogir and the rest of Croatia became part of the State of Slovenes, Croats and Serbs and subsequently, the Kingdom of Yugoslavia. During this period Italian speaking people, who until 1918 were among the city dwellers, left for Italy. Trogir was annexed by Italy during World War II. Subsequently, Tito's Partisans liberated it in 1944. After that, it yet again became a part of Yugoslavia, and since 1991 it has been part of Croatia.