Chiapas

The original franchise was founded on 27 June 2002 after the Tiburones Rojos de Veracruz franchise was sold and moved to Tuxtla Gutiérrez, Chiapas. They played their first game on 3 August, against Tigres UANL, losing 1–3 at home, with Lucio Filomeno scoring the club's first ever goal. The club's first win came on 25 August, beating San Luis 1–0. They finished the Apertura 2002, with a record of three wins, seven draws, and nine defeats. In the Clausura 2005 they finished with six wins, four draws, and seven defeats, and the head coach José Luis Trejo was sacked in the middle of the season. The club then named Antonio Mohamed as manager, but poor results meant another change with Fernando Quirarte taking over for the remainder of the season, bringing stability to the team and results improved. They won the Chiapas Cup in 2004 and on 16 July 2005, they won the Chiapas Cup for a second time, by defeating Necaxa at the Estadio Víctor Manuel Reyna. In February 2008, Sergio Almaguer was named manager of Chiapas.

In the Clausura 2006, under new coach Eduardo de la Torre, the club finished with the second best record over the regular season, and with it a place in the Play-offs, where they lost in the Quarter-finals to Guadalajara.

On 20 May 2013, the club was sold to Grupo Delfines whose majority stake holder Amado Yañez is also owner of Querétaro. Stating low attendance and lack of sponsorship, the new owner announced he would be moving the team to the city Querétaro, Querétaro to replace Querétaro recently relegated to the Segunda División de México. The owner added the fans of Querétaro deserved a top division club in their city.

On 20 May 2013, it was announced that the Jaguares de Chiapas franchise was sold and moved to the city of Querétaro, Querétaro. On 28 May 2013, it was announced San Luis was moved to the city of Tuxtla Gutiérrez, Chiapas and was renamed as Chiapas Fútbol Club, thus bringing back a Primera División de México team back to Chiapas. The new Chiapas franchise took over the San Luis television contract with Televisa. At the conclusion of the Clausura 2017 tournament, Chiapas F.C. was relegated to the Liga de Ascenso de México after finishing last in the relegation table.

On 8 June 2017, the team was dissolved after the owner of Chiapas, Carlos López Chargoy met with their coaching staff and players. However, a week later, the president of the Liga MX announced that the team was disaffiliated and made bail to pay what was due. The next day, a soccer team would return to Chiapas, but it would have to play in the Liga Premier. Jiquipilas Valle Verde F.C. announced on 23 June that it would change its franchise from Jiquipilas to Tuxtla Gutiérrez, naming the team Chiapas Jaguar and playing their home games at Estadio Víctor Manuel Reyna, but four days later, this did not happen because the FMF prohibited it to use the name, which the family Lopez Chargoy owns.

At the end of Clausura 2024, a rumor arose that the management of the Cimarrones de Sonora team was seeking to negotiate the transfer of the franchise to Tuxtla Gutiérrez, Chiapas to revive Jaguares F.C. Finally, on 30 May 2024, Juan Pablo Rojo –president of Cimarrones– announced through a statement that the institution was in the process of selling the membership certificate corresponding to the Liga de Expansión MX. However, the sell was not completed, and it was announced that the team would continue playing in Hermosillo, Sonora.

On 12 July 2024 the project was rejected by the Liga de Expansión owners assembly, so finally Jaguares F.C. began competing in the Liga Premier - Serie A, using the place that Cafetaleros de Chiapas had in the league and that was originally going to be used for a reserve squad of Jaguares F.C.