Atlético Nacional Femenino was founded as a youth academy team on 25 August 2009, with the project being led by manager Diego Bedoya and supported by Víctor Marulanda.

[3] On 10 February 2018, Atlético Nacional played their first match in the professional women's football league, defeating Real Cartagena by a 2–0 score.

[5] The club made it to the knockout stages of the domestic league in the subsequent seasons: in 2019 and 2020, Atlético Nacional reached the quarter-finals, being knocked out by América de Cali both times, and in 2021 they were defeated by Santa Fe in the semi-finals.

On 15 December 2022, Atlético Nacional Femenino signed an alliance with amateur club Formas Íntimas aiming to form a competitive team to take part in the 2023 Colombian Women's Football League.

[7] Under the alliance with Formas Íntimas, the club once again reached the semi-finals in the domestic league and qualified for the 2023 Copa Libertadores Femenina, in which they ended in third place.