He had little schooling.
As a young man he served as a notary public. In 1821 he entered politics and four years later was appointed secretary general of the government of Honduras. He ruled during the exile of the president and vice-president, who in 1826 had been overthrown by Manuel José Acre, president of the Central American Confederation, a loosely knit union of Central American states. Morazán organized forces to rid Honduras of Acre and defeated him in the battle of Trinidad, November 11, 1827. He reestablished representative government in Honduras and was made its provisional head. In the battle of Gualcho, Guatemala, July 6, 1829, Morazán again defeated Acre. At the head of an army he had entered Guatemala City, April 12, 1829, and assumed dictatorial power.
He was elected president of the Central American Confederation in March 1830 and suppressed a rebellion against its government. On March 28, 1832, Morazán took the city of San Salvador by assault. For a few years Morazán ruled in relative peace before the Central American Confederation fell apart in 1839. Morazán defeated the allied forces of Honduras and Nicaragua at Espiritu Santo, April 6, 1839, and was chosen president of El Salvador on July 18 of that year. He immediately invaded Honduras but was defeated early in 1840. To save himself and his government he invaded Guatemala and on March 18, 1840, took Guatemala City. Soon thereafter Morazán was overthrown by the factions that opposed him.
He went into exile, first in Panama and subsequently in Peru, but in 1842 he returned and took command of insurgent Costa Rican troops. He entered San José, Costa Rica, and was chosen president July 11, 1842, but was faced with bitter opposition. Besieged in San José, he tried to escape but was captured and executed on September 15, 1842.