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Origins and first Merida franchise

The team emerged in 1988 as the "Venados de Yucatan", when Mr. Jorge Arana Palma, acquires the franchise of the Second Division of the Alacranes de Apatzingán, and it is during this stage when the colors that would identify them to this day are defined, green, yellow and white. During this first season, they were runner-up in the Second Division in the 1988-89 season and the First Division 'A' championship in 1998.

Return of the Mérida

Mérida F.C. was returned in 2003 by the brothers Arturo and Mauricio Millet Reyes, who obtained the franchise of Nacional de Tijuana.

Loss of franchise in 2005 and continuation at lower levels

After the Clausura 2005 tournament, the Millet brothers announced that they would be selling the team to Irapuato FC due to economic problems, citing lackluster attendance and poor support from the local government. Nevertheless, the brothers formed a team that participated in an amateur league in Yucatán and also opened a training facility in Argentina to scout local talent. Mérida F.C. returned to the professional ranks when they participated in the Tercera División in 2006/07. During 2007, the brothers oversaw the construction of a training facility located at the Unidad Deportiva Tamanché. By the 2007/08 season Mérida was participating in the Segunda División.

Return of second level franchise with Morelia

On June 16, 2008, Arturo Millet Reyes announced that he had acquired the filial team of Morelia. Millet Reyes has stated that his intention is to maintain the team in Mérida for an extended period of time, unlike in previous years. He also received a guarantee that if the Venados were to be promoted to the Primera División that the team would remain in Mérida.

On November 11, 2008, the Federación Mexicana de Fútbol Asociación (FMF) granted the club the certification required to be promoted to the Primera División.

In the Clausura 2009 season Mérida defeated Club Tijuana 1–0 on aggregate to win the Clausura title. Mérida lost the subsequent promotion play-off for the Primera Division de Mexico, after a defeat by Querétaro FC on penalties.

Sale of franchise to Atlante

On 4 December 2010 the brothers Arturo and Mauricio Millet Reyes announced that Mérida F.C. would no longer form part of the Liga de Ascenso and that Monarcas Morelia would decide if a team would stay in the city, but that talks were also underway with Atlante F.C. regarding the creation of a link with them.

The Mérida franchise was subsequently sold to Atlante and they became that team's filial team for the Clausura 2011, whilst the original Atlante filial team (Atlante UTN) swapped franchises to become the subsidiary team for Morelia.