The 2012–13 season is C.D. Motagua's 62nd season in existence and the club's 47th consecutive season in the top fight of Honduran football. The domestic league will be divided into two tournaments, Apertura and Clausura. The Apertura was scheduled to be played in the second half of 2012, while the Clausura in the first half of 2013. Motagua will be looking for its 13th domestic championship. Due to an unsuccessful 2011–12 season, the club won't have international participation.

To be played from August to December 2012. On 8 May 2011, the fitness coach Juan Bertani announced his departure from the club, one day earlier José Treviño was confirmed as manager for the third consecutive tournament. The first player to sign for the club was César Oseguera who played as midfielder for Atlético Choloma last season. One day later on 10 May, Brazilian forward Jocimar Nascimento returned to the eagles, Jocimar was a key player for the club from 2006–2009. On the same day, midfielder Abner Méndez joined from C.D.S. Vida.

On 14 May, Motagua acquired 21-year-old forward Eddie Hernández who had a fleeting passage on Sweden with BK Häcken; Hernández is also part of the U-23 national team that will play at the 2012 Summer Olympics. The first player to left the team was Sergio Mendoza on 12 May; Julio de León was also released on 15 May. Roger Mondragón joined Vida on loan, as well as Adán Ramírez who was loaned to C.D. Real Sociedad. After 3 tournaments and one goalscorer award with the blues, Jerry Bengtson signed a 4-year agreement with MLS club New England Revolution.

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