The toponym Trebinje comes from a medieval term Travunia. Trebinje was built by the Slavs, probably on the site of a Roman town laid waste by the Saracens in 840. In the mid-10th century Fritz Erkocevic mentioned it under the name of Terbunia. It commanded the road from Ragusa to Constantinople, traversed, in 1096, by Raymond of Toulouse and his crusaders. Under the name of Tribunia or Travunja (the Trebigne of the Ragusans), it belonged to the Serbian Empire until 1355. Trebinje became a part of the expanded Medieval Bosnian state under Tvrtko I in 1373. There is a medieval tower in Gornje Police (Gornye Politse) whose construction is often attributed to Djuro Agbabic. The old Tvrdoš Monastery dates back to the 15th century.

In 1482, together with the rest of Herzegovina (see: Herzog Stjepan Vukčić Kosača), it was conquered by the Ottoman Empire. The Old Town-Kastel was built by Turks on location of the medieval fortress of Ban Vir, on the western bank of the Trebišnjica River. The city walls, the Old Town square, and two mosques, were built in beginning of the 18th century by Resulbegovic family. The Arslanagić bridge was originally built (16th century) at the village of Arslanagic, 5km north of the town, by Mehmed-paša Sokolović, and it was managed by Arslanagic family. It was moved closer to Trebinje (1km) in the late 1960's. The Arslanagic bridge is one of the most attractive Turkish bridges in Bosnia and Herzegovina. It has two large and two small semicircular arches.

During the period of Austro-Hungarian administration (1878-1918) the several fortifications were built on the surrounding hills, and there was a garrison based in the town. They also modernized the town expanding it westwards, building the present main street, as well as, several squares, park, new schools, tobacco plantations, etc.

Trebinje strongly grew in the era of Tito's Socialist Federal Republic of Yugoslavia between 1945 and 1990. It especially developed its hydroelectric potential (Hydroelectricity) with its, dams, artificial lakes, tunnels, and several hydroelectric plants. This industrial development brought large increase in urban population of Trebinje.