He was descended from a French West Indian family, received only a primary education from his uncle, the parish priest of Texiguat, and entered into business. When the independence of his country was declared in 1821, he began to take an active part in politics. The president of Honduras, Dionisio Herrera, appointed him secretary-general, and as such, he assisted in the organization of the State, and was afterward elected member of the first representative council.
In 1832 the chief of the state of Salvador, Cornejo, rebelled against the Federal government, and Francisco Morazan personally marched against, and defeated him at Jocoro on 14 March, occupying the city of San Salvador on 28 March. In 1838 a revolution began in Guatemala under the leadership of Carrera (q. v.), and Morazan marched against him ; but, as he feared trouble in Honduras and Nicaragua also, he left in command Colonel Agustin Guzman (q. v.), who was forced to make a treaty with Carrera in Rinconcito on 23 December Morazan several times defeated the revolutionary forces in 1839, but meanwhile Carrera, assisted by the clergy and aristocracy, had overthrown the government of Guatemala.
Morazan, by forced marches, captured that city at the head of 1,300 troops from Salvador on 18 March, 1840, but was besieged next day by Carrera with 5,000 men, and evacuated the city after a twenty-two hours’ fight. Seeing the Federal power crumbling under the repeated revolutions, he resigned the executive on 5 April, and went to Peru with his principal followers. There he found assistance from political friends and Central American refugees, and, provided with arms and other resources, he invaded Costa Rica on 11 April, 1842, soon overthrew the government, and assumed the executive, lie was preparing an expedition to invade the other Central American republics for the re-establishment of federal unity, when the towns of Heredia, Alhajuela, and San Joss revolted, and he was delivered to the rebels and shot.