The rain destroyed houses and crops and forced thousands to leave their homes for temporary shelters.
Six people were killed in Honduras and 7,000 evacuated their homes, local authorities said. In Nicaragua, the government said 23,000 people were affected and that a fisherman was killed after his boat overturned. Two others drowned in a river.
The head of El Salvador's civil protection agency said two people were killed, one after a tree fell on a car, and 10 others were injured by a wall that collapsed.
One person died in Costa Rica and a child disappeared in Guatemala.
(With inputs from agencies.)