The 2016–17 season was F.C. Motagua's 66th season in existence and the club's 51st consecutive season in the top fight of Honduran football. The club announced the continuation of Diego Vásquez as the team's head coach for his 4th consecutive season.

This season, the club fought for its 14th league and 2nd domestic cup. During the preseason, a new badge was unveiled to be used starting this season. On 2 July, the club's president Eduardo Atala confirmed an exhibition game against current Copa Libertadores winners at that time and South American giants River Plate. The game was played at Orlando, United States.

The Apertura schedule was unveiled on the second week of July and the club decided to return their home games on Sundays afternoon after their last season experiment of playing on Saturdays seeking for better assistances didn't throw the expected results. In week 6, Motagua faced C.D. Social Sol at home; in the 50' minute (0–0), the referee decided to suspend the match due to heavy rain which caused a power outage. The remaining 40 minutes were played the following morning, landing in the club's 88th anniversary. Román Castillo who had lost his younger brother a week prior, decided the match with a late goal at the 90th+5 minute. On 25 September, Motagua had to move its home game against C.D. Honduras Progreso to Catacamas due to a religious event that took place at Estadio Tiburcio Carías Andino. This match at Catacamas marked history in the Honduran Liga Nacional as the first game ever officiated by a female referee. On week 17, a 2–2 away tie against Real C.D. España defined Motagua's 4th place in the regular season standings and therefore, a berth to the playoffs phase. Once in the playoffs, Motagua defeated C.D. Marathón away in postseason for the first time since November 1990; however, the access to the semifinals didn't turned out that easy as Motagua had to rely on a late and controversial penalty in the second leg to advance with a 3–3 global score. In the semifinals Motagua faced city rivals Club Deportivo Olimpia for another edition of the Honduran Superclásico, resulting in the fourth time these two teams meet in this stage in the last three years. With a 2–1 aggregated score, Motagua moved on and qualified to their 19th league final in history. On 18 December, Motagua obtained their 14th national championship after defeating Platense F.C. in an unprecedented final. It was also the first time a league title was decided at Puerto Cortés. With the win, the team secured a spot for the 2017–18 in CONCACAF club competitions.

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