Former president Manuel Zelaya was overthrown in a coup after trying to end the one-term limit
"I am going to be the next president of Honduras," Hernandez said triumphantly in a speech to some 10,000 supporters at a baseball stadium east of the capital Tegucigalpa.
"This event marks a before and an after," the conservative leader said to cheers and applause.
Hernandez, 48, said he would run on his record of fighting the violent crime that made Honduras one of the most murderous countries in the world.
"In three years we have improved security" after being "the most violent country on the face of the Earth," he said.
Honduras's 1982 constitution limits presidents to a single four-year term.
It even strips the citizenship of anyone who promotes changing the law to allow re-election.
But Hernandez's National Party, which also controls Congress, says a Supreme Court ruling last year allows him to stand for a new term.
The opposition disagrees, arguing the court does not have that power.
It is a loaded debate in the Central American country, where former president Manuel Zelaya was overthrown in a coup in 2009 after the leftist leader tried to hold a non-binding referendum on ending the one-term limit.
The next presidential election is set for November 2017. Hernandez's term ends the following January.