In 1995, a team named Atlético Nacional was founded and played a couple of years in the ANAPROF league until they were disbanded in 2001 due to manipulation and alteration of documents.

In 1996–97 the club played a modest season after just coming 1 point short of reaching the hexagonal round of ANAPROF, it finished 8th of 12 teams.

2001 was the last season of Atletico Nacional, after the league was reformatted and divided into Apertura and Clausura championships, the team never managed to get into the hexagonal round.

In December 2012, Atlético Nacional lost the Apertura final to Millenium UP[5] but they clinched promotion to the LPF in June 2015 after they won the Panamanian Second Division championship decider against SUNTRACS.

[7] Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.