Seeking safety at the Brazilian Embassy, Zelaya called on his countrymen to come to the capital for peaceful protest.
"It is the moment of reconciliation," he said Monday during a televised speech that featured Zelaya's voice but not his image.
His surprise arrival sparked demonstrations in the streets outside the embassy as supporters, who have protested for months since his ouster, cheered his return.
"We are all happy, because he is the constitutional president of Honduras," teacher Alfredo Rodriguez Escobar told The Associated Press. Overhead a police helicopter hovered over the growing crowd.
The return sharply and suddenly escalates the country's political crisis - challenging the government installed by the coup to make good on its promise to arrest Zelaya and making him a polarizing figure for demonstrations - for and against -directly in the country's capital.
The country's Congress and Supreme Court, alarmed by Zelaya's political shift into a close alliance with Venezuelan President Hugo Chavez, backed Zelaya's removal, arguing that he violated the constitution, even if many officials say he should have been arrested rather than sent abroad.
Crowds gathered outside the United Nations compound early Monday after Zelaya initially went on television saying he had arrived there, apparently trying to mislead local officials. He later appeared at the Brazilian Embassy.
Zelaya said he had "evaded a thousand obstacles" to return. And his staunch supporter, Chavez, described the journey: "President Manuel Zelaya, along with four companions, traveled for two days overland, crossing mountains and rivers, risking their lives. They have made it to Honduras."
Zelaya was forced out of the country at gunpoint on June 28. Interim leader Roberto Micheletti has repeatedly said a jail cell awaits Zelaya if he comes back.
Most international leaders - including the United States and the Organization of American States - say they still recognize Zelaya as president and demand he be reinstated.
Micheletti has said he will step aside after presidential elections are held as scheduled in November.
If the interim administration attempts to imprison Zelaya, protesters who have demonstrated against his ouster could turn violent, said Vicki Gass at the Washington Office on Latin America.
"There's a saying about Honduras that people can argue in the morning and have dinner in the evening, but I'm not sure this will happen in this case," said Gass. "It's been 86 days since the coup. Something had to break and this might be it."
But Juan Carlos Hidalgo, project coordinator for Latin America at the libertarian Cato Institute, said Zelaya should expect to be jailed.
"If he is back, his options are quite limited, because the moment that his location is discovered or that he publicly comes out of the trees where he's hiding, he's going to be arrested for sure," he said.
--- Associated Press reporters Catherine E. Shoichet, Martha Mendoza and Alexandra Olson in Mexico City and Fabiola Sanchez in Caracas, Venezuela, contributed to this report.