The club was founded on 7 March 1997 as Centro de Treinamento Uniclinic,[2][3] and played their first senior tournament took place in 1998, as they featured and won the Campeonato Cearense Second Level.

In 2016, the club reached the finals of the Cearense, but lost the title to Fortaleza; later in the year, the club debuted in a national competition after featuring in the Série D. During the 2017 campaign, Uniclinic made their debut in the Copa do Brasil and in the Copa do Nordeste, being knocked out in the first stage of both tournaments.

[5] On 17 October 2021, Atlético Cearense achieved promotion to the Série C for the first time in their history, after a 4–3 penalty win over Ferroviária.

[6] Atlético Cearense is the owner of Estádio Antônio Cruz, which has a capacity of 3,000 people.

[1] The club often play their most important home games at Estádio Presidente Vargas,[3] which has a maximum capacity of 20,262 people.