In 12 February 1917, the brothers Román Alday and Gerardo Ferrat alongside Filiberto Navas and Manuel Henkel created Deportivo Toluca Futbol Club. In 1950, the team joined the recently formed Segunda División, advancing to Mexican Primera División in 1953 by having tied with Irapuato by three goals, two by Rubén Pichardo and one by that tournament's goal scorer Mateo de la Tijera having left one more match to play.
The Teams first official First Division game was against Atlante, in which Toluca won 2 goals by one
The team won three consecutive championships in 1966 and 1967 under coach Ignacio Trelles. In 1975 Toluca won the championship one more time. Coached by Uruguayan Ricardo de León, Toluca played a style of game that was consistently criticized as ultra-defensive but won the championship by defeating León in the final-four mini-tournament 1-0, with the lone goal being scored by Ecuadorian Ítalo Estupiñan. This is the only time the Mexican Championship has been decided by a round-robin, two-legged, mini-tournament.
In 1997 Enrique "Ojitos" Meza became the coach of the team, after reaching the finals of the Mexican league with Toros Neza. Toluca resurged, its tactical scheme was very offensive, which was very characteristic of its coach. It was not atypical to see scores like 5-3. The offensive idea suited perfectly the Paraguayan José Saturnino Cardozo, who became the best scorer of the league in four occasions.
Toluca won the championship in 1998, the first one in twenty years. With Enrique Meza as coach, Toluca won the championship three times in a period of three years.
In the Invierno 2001 tournament Ricardo La Volpe became the coach of Toluca. He, along with Cardozo and Vicente Sánchez had one of the most successful and exciting teams in years. However, La Volpe left Toluca with a few weeks left in the season, but without him, they still won their 7th title.
At the end of the Apertura 2005 tournament, the team became champions again, beating Monterrey by an aggregate of 6-3, after the questionable decisions of Mexican referee Marco Rodriguez "El Chiquidracula", who expelled three players from Monterrey on their first foul committed.
In the Clausura 2007 tournament, Toluca had one of their worst seasons, finishing in last place. In the Copa Libertadores 2007, they made it to the round of 16, where they were subsequently eliminated by Cúcuta Deportivo from Colombia. Following the elimination from both tournaments, Gallego resigned from his position stating the need for a year off as his reason for resigning from Club Toluca. José Pekerman, former coach of the Argentine national team, was appointed as head coach of Club Toluca on May 30, 2007. In the Apertura 2007, Toluca had a much better finish than the previous tournament, placing 2nd place out of 18 only behind league leader Santos Laguna. They were ultimately eliminated by league runner-up Pumas in the quarter-finals of the Apertura 2007 playoffs.
Club Toluca failed to qualify for the 2008 Copa Libertadores. On the Apertura 2008, Toluca had a weak start under their new coach, Jose Manuel "El Chepo" De La Torre, on one point going on a four game streak of only draws. On the last five games of the regular season, they reversed the tying streak, making 13 points out of a possible 15, ending the regular season in 2nd place overall with 27 points and thus advancing to the playoffs. Their goalkeeper Hernan Cristante set a record by not allowing any goals for 773 minutes. Toluca would go on to win the Bicentenario 2010 tournament by beating Santos Laguna in a dramatic penalty shoot-out, earning them the tenth cup win, the same amount as Club América. Besides winning the domestic title ten times, Toluca has also been the Runner-Up of the Mexican domestic tournament six times. On the Apertura 2012, Toluca finished first place and therefore earned a place for the Copa Libertadores. On the Ligullia of the Apertura 2012, Toluca went all the way to the final and lose to Club Tijuana 4-1 aggregate. On the Cluasura 2013, Toluca finished 13th and did not qualify for the Ligullia. At the end of that season then coach Enrique Meza resigned his job. The next day Toluca contacted its top scorer former player Jose Cardozo as its new head coach.
In the new era of Jose Cardozo as head coach, Toluca went to be the most offensive club in the Apertura 2013 with 33 goals and receiving 17 goals. In the Apertura 2013 Pablo Velázquez became the league's goal scorer with 12 goals. In that season Club Toluca ended in the semifinals losing to Club America in away goals. In the next season being the Clausura 2014, Club Toluca became the most defensive club in the league with 14 goals scored against and scoring 25 goals and came second in the league and lost to Club León in the semifinals.