The club was founded on 29 August 1928. Three previous clubs, América,
Honduras Atlética and Águila, were in the process of falling apart. Marco Antonio Ponce and Marco Antonio Rosa called a meeting and proposed that the clubs unite to form a new club, Motagua (named for a nearby river). After the success of the meeting, a board of directors was appointed. The first game was played on 25 November 1928, against
Tejeros del España at
La Isla. Constantine Gálvez "Tatino" was the captain and
Daniel Bustillo was the manager. The team fought to a 1–1 draw. The first international game was played on 9 April 1939 against Costa Rican side
Orión at the
San Felipe field in
Tegucigalpa; Motagua were managed by Honduran coach
Lurio Martínez and won the match 3–0 with three goals from
"Gorgojo" Ramos.
Professional Era The team debuted professionally in the
1965–66 season. It took them only three years to win their first-ever championship. Under the leadership of manager
Rodolfo Godoy, Motagua surged past two-time defending champions Olimpia to win the
1968–69 title, with 39 points to the Olimpia's 36. Godoy's club completed the double that season by winning the first-ever Honduran Cup. This was the beginning of a long run at or near the top of the table for Motagua; they finished second behind Olimpia in
1969–70, then won the
1970–71 crown. That last season ended with Motagua and Olimpia level on points, with Motagua hoisting the crown on goal difference. They would likely have won a third championship in
1972–73, as they led the table halfway through the season. However, the season was cancelled at its midway point, and the records expunged. The rest of the 1970s remained a good time for Motagua. They won titles in
1973–74 and
1978–79, while finishing second in
1974–75 and
1976–77. The club had become established as one of the nation's strongest, and when the
Honduras national football team qualified to the
World Cup Finals, they featured five Motagua players. However, the 1980s were not as strong. Between 1979 and 1992, the club was locked out of the Honduran crown. It wasn't until the end of the
1991–92 season that the drought was over. They claimed that title by beating Real España 1–0 in the championship playoffs. With the drought broken, Motagua began winning titles regularly. They claimed the Honduran Cup in 1993 and 1995, then claimed an unexpected championship in the 1998 Apertura, beating Real España 5–2 on aggregate in the championship final. They repeated as champions that October, beating Olimpia 1–0. They did it again in 1999–2000, beating Olimpia on penalties in both the Apertura and Clausura finals. They added another title in the 2002 Apertura, beating Marathón on penalties in a thrilling 5–3 shootout. After a drought of nearly five years, Motagua returned to the top with a title in the 2006 Apertura (over Olimpia) and 2011 Clausura (again over Olimpia). In 2013, a new golden age began.
Diego Vásquez, a veteran Honduran keeper who had played in two stints for Motagua, took over. In just his second full season, Vasquez steered Motagua to the 2014 Apertura crown, beating Real Sociedad 2–1 in the championship final (Rubilio Castillo's header was the winner). Three near misses followed, but in 2016–2017, Vasquez would lead the team to new heights. It started with the 2016 Apertura. After taking 4th in the regular season, Motagua battled their way through the quarterfinals and semi-finals (beating Olimpia). Then they held off Platense 2–1 on aggregate to win the Apertura title. In the Clausura, they finished 2nd in the regular season, then stormed to the title, crushing Honduras Progreso 7–1 on aggregate. Vasquez, who remains Motagua's manager, is the longest tenured manager in the history of Honduras's top-flight; he has managed 200 consecutive matches with Las Aguilas. Overall, between both amateur and professional seasons, Motagua has won 27 titles. They have won 16 professional titles. The club has participated in all
Honduran top division seasons since its inception in 1965 and is one of the few
unrelegated teams. ==The club==