Self-educated, Morazán began his political career in his native Honduras. In 1827, at age 35, he led the Liberal Party's forces in a revolt against Manuel José Arce, first president of the United Provinces (established in 1823). The Liberal forces defeated the Conservative army in 1829) at Guatemala City, the capital, and in 1830 Morazán was elected president. He introduced many reforms designed to limit the power of the Roman Catholic Church, but his administration aroused the anger of Conservatives and he had to devote most of his energy to putting down revolts.

By 1839, the end of Morazán's second term, most of the member states had deserted the federation. A Conservative-backed rebel army under Rafael Carrera defeated Morazán at Guatemala City in March 1840, and he went into exile. In 1842 he returned to attempt the restoration of the federation. He attacked and defeated the forces of the Costa Rican dictator Braulio Carillo, but, when he tried to follow up this triumph, his forces were quickly routed. Betrayed and captured, Morazán was executed by a firing squad.