It comes after regional leaders met in Jamaica on Monday to discuss a political transition in Haiti.
Mr Henry is currently stranded in Puerto Rico after being prevented by armed gangs from returning home.
In a video address announcing his resignation, Mr Henry urged Haitians to remain calm.
“The government that I am leading will resign immediately after the installation of [a transition] council,” Mr Henry said.
“I want to thank the Haitian people for the opportunity I had been granted. I’m asking all Haitians to remain calm and do everything they can for peace and stability to come back as fast as possible.”
Mr Henry, who had led the country supposedly on an interim basis since July 2021 following former President Jovenel Moïse’s assassination, had repeatedly postponed elections, saying security must be restored first.
