Thapsus was founded by Phoenician traders on Ras ed-Dimas, a promontory on Tunisia's Mediterranean coast that was easy to defend and strategically positioned on the sea routes between the Strait of Gibraltar and the Phoenician homeland. A salt lake lay nearby, providing a valuable commodity for trade. The city sat roughly 135 kilometers from the island of Lampedusa and approximately 200 kilometers southeast of Carthage, close enough to the great Punic capital to be drawn into its orbit but far enough to maintain its own commercial identity. Diodorus Siculus records that Agathocles of Syracuse conquered the city during his wars against Carthage, but Thapsus endured, adapting to each new master.

In 46 BC, the fields around Thapsus became the stage for one of the most consequential battles of the Roman civil war. Julius Caesar, pursuing the last organized Republican opposition, confronted the forces of Metellus Scipio and the Numidian king Juba I. The Battle of Thapsus was costly, but Caesar's victory was decisive. It ended organized resistance against him in Africa. Caesar extracted a payment in sesterces from the defeated city, a reminder that mercy in the Roman world was transactional. Thapsus subsequently became a Roman colony in the province of Byzacena, its Phoenician past subsumed into the administrative machinery of the empire.

The harbor mole at Thapsus was an enormous engineering project, a breakwater of Roman concrete and stone stretching nearly a kilometer into the sea. It may have been begun by the local emperors Gordian II and Gordian III, whose reigns were too brief to see it completed. The construction was possibly abandoned partway through. Thapsus was never a major port; after the collapse of neighboring Thysdrus in the third century, maritime trade in the region shifted to harbors at Sullecthum, Thaenae, Leptis, and Gummi. The mole became an artifact of unrealized ambition, a testament to what the city wanted to be rather than what it became. Most of it now sits beneath the waves, detectable but no longer functional.

Thapsus was the seat of a Christian bishopric during the Roman era, and its most notable bishop was Vigilius, who authored controversial works against the Arians and Eutychians. In 484, the Vandal king Hunneric summoned the Catholic bishops of North Africa to his court in Carthage and then exiled them; Vigilius was among those punished for refusing to accept Arian theology. The ruins that survive today include an amphitheatre and mosaics, and in 2022, geophysical survey detected the possible location of a theater. The Catholic Church reestablished the bishopric as a titular see in 1914, an honorary designation that has passed through a succession of holders, keeping the name of Thapsus alive in ecclesiastical records even as the physical city dissolved into the landscape near modern Bekalta.