Envigado FC U20

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 has not been relegated ever since, although they played relegation play-offs in 2008 and 2010, defending 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.

In November 2014, Envigado F.C. and its major shareholder Juan Pablo Upegui were included into the Specially Designated Nationals and Blocked Persons List (also known as the Clinton List) by the United States's Office of Foreign Assets Control (OFAC) due to their links with the drug cartel Oficina de Envigado (Envigado Office). Although not all of the club's transactions were found to be illicit, the U.S. Treasury verified that the club had been used by the organization for money laundering, after 10 years of investigations. 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.