Amazonas Futebol Clube was first idealized in 2017 and officially founded on 23 May 2019. The founding of the club was headed by businessman Wesley Couto — who heads the club as president — William Abreu, former football director of Atlético Rio Negro Clube, and Roberto Peggy, former president of Nacional Futebol Clube, both of which are traditional clubs from Manaus. The objective was organizing a competitive club and revitalizing football in the state of Amazonas.
Amazonas FC played their first professional tournament, the Campeonato Amazonense Second Division, nearly six months later. They won the tournament after defeating São Raimundo in the final.
In their first Campeonato Amazonense, Amazonas FC were knocked out in the first phase. In 2021, after Manaus FC reached the finals, the club qualified to the 2022 Série D for the first time in their history, after being the best-placed team in the first phase.
On 28 August 2022, Amazonas achieved a first-ever promotion to the Série C, after defeating Portuguesa-RJ in the 2022 Série D quarterfinals.
After their promotion one year before, Amazonas beat Botafogo-PB 2-0 and won the club's first ever promotion to the second division. On 22 October 2023, Amazonas became champions of Série C, the first national title for a team from the state of Amazonas.