"Originally a Thracian settlement, known as Menebria, the town became a Greek colony when settled by Dorians from Megara at the beginning of the 6th century BC. At 425-424 BC the town joined the Delian League, under the leadership of Athens. The town fell under Roman rule in 71 BC.

In the medieval era it was one of the most important strongholds of the Byzantine Empire from the 5th century AD onwards, and was fought over by Byzantines and Bulgarians, being captured and incorporated in the lands of the First Bulgarian Empire in 812 by Khan Krum after a two-week siege only to be ceded back to Byzantium by Knyaz Boris I in 864 and reconquered by his son Tsar Simeon the Great. During the time of the Second Bulgarian Empire it was also contested by Bulgarian and Byzantine forces and enjoyed particular prosperity under Bulgarian tsar Ivan Alexander (1331–1371) until it was conquered by Crusaders led by Amadeus VI, Count of Savoy in 1366. The Bulgarian version of the name, Nesebar or Mesebar, has been attested since the 11th century.

The capture of the town by the Turks in 1453 marked the start of its decline, but its architectural heritage remained and was enriched in the 19th century by the construction of wooden houses in style typical for the Bulgarian Black Sea Coast during this period.After the Liberation of Bulgaria from Ottoman rule in 1878, Nesebar became part of the autonomous Ottoman province of Eastern Rumelia in Burgaz department until it united with the Principality of Bulgaria in 1885. It developed as a key Bulgarian seaside resort since the beginning of the 20th century. After 1925 a new town part was built and the historic Old Town was restored."

Nesebar is sometimes said to be the town with the highest number of churches per capita. Total of forty churches survive, wholly or partly. There are the most famous of them:

• Church of St Sophia or the Old Bishopric
• Basilica of the Holy Mother of God Eleusa
• Church of Christ Pantocrator
• Church of the Holy Archangels Michael and Gabriel