Although all of Honduras lies within the tropics, the climatic types of each of the three physiographic regions differ. The Caribbean lowlands have a tropical wet climate with consistently high temperatures and humidity, and rainfall fairly evenly distributed throughout the year. The Pacific lowlands have a tropical wet and dry climate with high temperatures but a distinct dry season from November through April. The interior highlands also have a distinct dry season, but, as is characteristic of a tropical highland climate, temperatures in this region decrease as elevation increases.

Unlike in more northerly latitudes, temperatures in the tropics vary primarily with elevation instead of with the season. Land below 1,000 meters is commonly known as tierra caliente (hot land), between 1,000 and 2,000 meters tierra templada (temperate land), and above 2,000 meters tierra fría (cold land). Both the Caribbean and Pacific lowlands are tierra caliente, with daytime highs averaging between 28° C and 32° C throughout the year. In the Pacific lowlands, April, the last month of the dry season, brings the warmest temperatures; the rainy season is slightly cooler, although higher humidity during the rainy season makes these months feel more uncomfortable. In the Caribbean lowlands, the only relief from the year-round heat and humidity comes during December or January when an occasional strong cold front from the north (a norte) brings several days of strong northwest winds and slightly cooler temperatures.

The interior highlands range from tierra templada to tierra fría. Tegucigalpa, in a sheltered valley and at an elevation of 1,000 meters, has a pleasant climate, with an average high temperature ranging from 30° C in April, the warmest month, to 25° C in January, the coolest. Above 2,000 meters, temperatures can fall to near freezing at night, and frost sometimes occurs.

Rain falls year round in the Caribbean lowlands but is seasonal throughout the rest of the country. Amounts are copious along the north coast, especially in the Mosquitia, where the average rainfall is 2,400 millimeters. Nearer San Pedro Sula, amounts are slightly less from November to April, but each month still has considerable precipitation. The interior highlands and Pacific lowlands have a dry season, known locally as "summer," from November to April. Almost all the rain in these regions falls during the "winter," from May to September. Total yearly amounts depend on surrounding topography; Tegucigalpa, in a sheltered valley, averages only 1,000 millimeters of precipitation.

Honduras lies within the hurricane belt, and the Caribbean coast is particularly vulnerable to hurricanes or tropical storms that travel inland from the Caribbean. Hurricane Francelia in 1969 and Tropical Storm Alleta in 1982 affected thousands of people and caused extensive damage to crops. Hurricane Fifi in 1974 was the worst natural disaster in recent Honduran history; more than 8,000 people were killed, and nearly the entire banana crop was destroyed. Hurricanes occasionally form over the Pacific and move north to affect southern Honduras, but Pacific storms are generally less severe and their landfall rarer.

Data as of 1993