Although there is evidence of Maya presence in Copan as early as 1000 BC, Christopher Columbus set foot on the American mainland for the first time at Trujillo in northern Honduras in 1502. He named the country after the deep water off the Caribbean coast; Honduras means depths.

The Spanish settled in Trujillo, on the north coast of Honduras, in 1525, but soon moved to the cooler highlands, where they established a capital at Comayagua in central Honduras in 1537, and this remained the political and religious center of the country for 350 years, until Tegucigalpa became the capital in 1880.

The Indians resisted Spanish colonialism, and, by some accounts, almost managed to drive the colonizers from the mainland. The chief of the Lenca tribe, Lempira, led 30,000 Indians against the Spanish, but was treacherously murdered at peace talks in 1538, and by the following year resistance was crushed. Gold and silver were discovered near Tegucigalpa in 1570, attracting British and Dutch pirates to the Trujillo area.

Around 1600, the Spanish estimated that Roatan was home to 5000 British buccaneers.

While Spain concentrated its energies on the interior, the British were attracted to the Caribbean coast by the abundant mahogany found in the region. They imported black settlers from Jamaica and other West Indian islands to harvest the timber.

Following an appeal by chiefs of the Miskito Indians, a British protectorate was declared over the entire coastal region extending from Honduras into Nicaragua. This lasted until 1859, when the area was relinquished to Honduras.

In 1969, Honduras and El Salvador had a brief war known as the Soccer War, which resulted in El Salvadoran troops invading Honduran territory and bombing Honduran airports. The war, which took place during a World Cup qualifying soccer match between the two countries, was sparked by the alleged mistreatment of El Salvadoran immigrants in Honduras. It lasted only 100 hours.

In November 1998, international aid and relief workers poured into Central America to help with the recovery from the devastation left by Hurricane Mitch. Honduras was the hardest hit by Mitch's rampage. The three days of rain that followed Mitch caused landslides and floods that buried towns and destroyed over 100 bridges throughout the country. When the Río Choluteca flooded, it devastated Tegucigalpa, the capital, sweeping things downriver and leaving behind an ocean of mud.