Historically known as Tawam or al Buraimi Oasis, Al Ain became a distinct location following independence in 1971. Al Ain has been inhabited for over 4,000 years, with archaeological sites showing human settlement at Al Hili and Jabel Hafeet. These early cultures built "beehive" tombs for their dead and engaged in hunting and gathering in the area. The oasis provided water for early farms until the modern age. A companion of the prophet Muhammad, Kaab Bin Ahbar was sent to the region to introduce Islam. He settled and died in the oasis.[2] The forts currently in Al Ain were built in the late 19th or early 20th century to solidify Abu Dhabi's control over the oasis.

Wilfred Thesiger visited Al Ain in the late 1940s during his travels across the Empty Quarter. He met Sheikh Zayed and stayed with him at Al Muwaiji Fort. This network of fortresses served as the trading and slaving posts for the area.

In 1952 Saudi Arabia sent raiders to capture Al Ain's fortresses and incorporate the oasis into the Saudi kingdom. Forces from theTrucial Oman Scouts as well as the army of Oman arrived to recapture the oasis. With British intervention, the Saudi forces withdrew, leaving the oasis back in the hands of Abu Dhabi and Oman.

Prior to independence, Al Ain was part of the Arabian slave trade network that extended from east Africa into the Persian Gulf. In the 1960s, Sheikh Zayed abolished formal slavery. Today, some families in both Al Ain and Buraimi are descended from these slaves.

In 1971 Queen Elizabeth II visited the Hilton Hotel, still in use, during her tour of the Persian Gulf. Following independence in 1971, Al Ain experienced rapid growth and investment as part of the emirate of Abu Dhabi, quickly becoming larger and more successful than Oman's Buraimi. In 1972 Oman and Abu Dhabi agreed on the final borders to divide Buraimi and Al Ain. Until Sheikh Zayed's death in 2004, Al Ain's municipal code forbade construction of buildings over four floors, with the exceptions of the Hilton, Intercontinental, and Rotana hotels.

In the 1990s, a serious uprising occurred among the laborers of the industrial district of Al Ain, as-Sanaiya. This uprising was suppressed by the UAE army and local police forces. All the laborers involved were interned and deported. Reportedly, UAE forces recovered caches of weapons during the suppression, although it's not known if there were any deaths.

Until 2006, Buraimi and Al Ain shared an open border. This border was closed in November 2006, and passport controls were imposed.