In the 6th century, Kallinikos became a center of Syriac monasticism. Deir Mār Zakkā, or the Saint Zacchaeus Monastery, sited on the tell just north of the city, today's Tall al-Bi'a, became renowned. A mosaic inscription there is dated to the year 509, presumably from the period of the foundation of the monastery. Deir Mār Zakkā is mentioned by various sources up to the 10th century. The second important monastery in the area was the Bīzūnā monastery or 'Dairā d-Esţunā', the 'monastery of the column'. In the 9th century, when ar-Raqqah served as capital of the western half of the Abbasid empire, this monastery became the seat of the Syriac Patriarch of Antioch.
In the year 18/639, the Muslim conqueror 'Iyāḍ ibn Ghanm took the Christian city Kallinikos by contract. Since then, it figured in Arabic sources as ar-Raqqah, but still in Syriac sources the name of Kallinikos remained. In 20/640-1, the earliest congregational mosque in the Jazira was build in the predominantly Christian city. many companions of the Prophet Muhammad used to live in ar-Raqqah. The strategic importance of ar-Raqqah grew during the wars at the end of the Umayyad period and the beginning of the 'Abbasid regime. Ar-Raqqah lay on the crossroads between Syria and Iraq and the road between Damascus, Tadmur (Palmyra), the temporary caliphal residence ar-Rusafa, ar-Ruha' (present day Urfa in Turkey) and the Byzantine and Caucasian theaters of raids and wars.
In 771-772 the Abbasid caliph al-Mansur built a garrison city about 200 metres to the west of ar-Raqqah for a detachment of his Khorasanian Persian army. It was named ar-Rāfiqah, "the companion". The strength of the Abbasid imperial military is still visible in the impressive city wall of ar-Rāfiqah.
Ar-Raqqah and ar-Rāfiqah merged into one urban complex, together larger than the former Umayyad capital Damascus. In 796, the caliph Harun al-Rashid decided for ar-Raqqah/ar-Rafiqah as his imperial residence. For about thirteen years ar-Raqqah/ar-Rāfiqah was the capital of the Abbasid empire stretching from Northern Africa to Central Asia, while the main administrative body remained in Baghdad. The palace area of ar-Raqqah covered an area of about 10 square kilometres north of the twin cities. One of the founding fathers of the Hanafi school of law, Muḥammad ash-Shaibānī, was chief qadi (judge) in ar-Raqqah. The splendour of the court in ar-Raqqah is documented in several poems, collected by Abu al-Faraj al-Isfahāni in his "Book of Songs" (Kitāb al-Aghāni). Only the small, restored so called Eastern Palace at the fringes of the palace district gives an impression of Abbasid architecture. 8 km west of ar-Raqqah lay the unfinished victory monument called Heraqla from the period of Harun al-Rashid. It is said to commemorate the conquest of the Byzantine city Herakleia in Asia Minor. Other theories connect it with cosmological events. Both theories must not contradict each other. The monument is preserved in a substructure of a square building in the centre of a circular walled enclosure, 500 m in diameter. However, the upper part was never finished, because of the sudden death of Harun al-Rashid in Khorasan. After the return of the court to Baghdad in 809, ar-Raqqah/ar-Rāfiqah remained the capital of the western part of the empire including Egypt.
Ar-Raqqah's fate declined in the late 9th century because of the continuous warfare between the Abbasids and the Tulunids and then with the Shii extremist movement, the Qarmatians. During the period of the Hamdānids in the 940s the city declined rapidly. At the end of the 10th century until the beginning of the 12th century, al-Raqqah was cantroled by Bedouin dynasties. The Banu Numayr had their pasture in the Diyār Muḍar and the 'Uqailids had their center in Qal'at Ja'bar.
Ar-Raqqah was destroyed during the Mongol wars in the 1260s. There is a report about the killing of the last inhabitants of the urban ruin in 1288.
The city of ar-Raqqah was resettled from 1864 onwards, first as a military outpost, then as a settlement for former Bedouin Arabs and for Chechens, who came as refugees from the Caucasian war theaters in the middle of the 19th century.
In the 1950s, in the wake of the Korean war, the world wide cotton boom stimulated an unpreceded growth of the city, and the recultivation of this part of the middle Euphrates area. Cotton is still the main agricultural product of the region.
The growth of the city meant on the other hand a removal of the archaeological remains of the city's great past. The palace area is now almost covered with settlements, as well as the former area of the ancient ar-Raqqa (today Mishlab) and the former Abbasid industrial district (today al-Mukhtalţa). Only parts were archaeologically explored. The 12th-century citadel was removed in the 1950s (today Dawwār as-Sā'a, the clock-tower circle). In the 1980s rescue excavations in the palace area began as well as the conservation of the Abbasid city walls with the Bāb Baghdād and the two main monuments intra muros, the Abbasid mosque and the Qasr al-Banāt.
There is a museum, known as the Ar-Raqqah museum, housed in an administration-building erected during the French Mandate.