The club was founded on 14 October 1989 and became the first team to earn promotion to the Colombian top flight as they won the inaugural
Categoría Primera B tournament, held in
1991. In that tournament, they topped the final group ahead of
Alianza Llanos,
Club El Cóndor, and
Atlético Huila. Envigado were able to consolidate themselves as a
Primera A team, reaching the final stages of the league for the first time in
1994 after placing eighth. They were eliminated in the semifinals, placing third in their group. They also made it to the final stages of the competition in the
2002 Apertura, in which they also placed third in their semifinal group, and the
2005 Apertura, in which they placed second in their group, one point behind the eventual finalists
Santa Fe. Envigado were relegated from the Primera A on 12 November 2006 after a 1–0 loss to
Cúcuta Deportivo on the final round of the
2006 Finalización tournament, thus ending a 15-year spell in the top flight, but quickly bounced back by winning the
2007 Primera B tournament with a team led by debutant playmakers
James Rodríguez and
Giovanni Moreno and managed by
Jesús Barrios. Envigado secured promotion back to the top flight by beating
Academia in the finals of both of the season's short tournaments. The team was at risk of relegation in the following seasons, playing relegation play-offs in
2008 and
2010, but they defended successfully their Primera A status in both of them. They made their best campaign in the top flight in the
2011 season, when they made it to the quarter-finals of both the Apertura and Finalización tournaments, which helped them place third in the season's aggregate table and achieve their first qualification for an international tournament, the
2012 Copa Sudamericana. There they were eliminated at the second stage after beating
Unión Comercio from Peru 2–0 on aggregate and losing to
Liverpool from Uruguay 2–1 on aggregate. Envigado was removed from the list on 26 April 2018, and shortly after it was announced that 55% of the club's shares had been sold to the equity fund ProFútbol. In
2025, and following poor campaigns in the preceeding seasons, Envigado ended a 17-year spell in the top flight as they were relegated to the second tier for the second time in their history. Their relegation was confirmed with six matches left in the season after they lost 2–1 to
Atlético Bucaramanga on 4 October. ==Honours==