Juan Carlos Chavez, 46, who spent the past 15 years on death row, was declared dead of lethal injection after 8:00 pm (0100 GMT today), said Florida prisons spokeswoman Misty Cash.
He was put to death two hours later than planned due to a last-ditch appeal that was ultimately rejected by the US Supreme Court.
Chavez admitted to kidnapping "Jimmy" Ryce at gunpoint as he got off the bus after school on September 11, 1995, and then raping him and beating him when the pre-pubescent boy tried to escape.
The owner, Susan Scheinhaus, found Chavez with the child's school bag and with a weapon she had reported stolen.
More From This Section
Ryce's dismembered body was later found buried in cement in the garden of a neighbouring farm, according to a court document.
In his last appeal to the Supreme Court, Chavez argued his constitutional rights to avoid "cruel and unusual punishment" would be violated if the state used the planned drug cocktail to put him to death.
In response, it has been using a new cocktail since October: midazolam to render the inmate unconscious, followed by two additional drugs to paralyse and kill.
Midazolam was used in a controversial execution last month in Ohio, where witnesses said the inmate appeared to suffer.
Several of those sentenced to death have recently asked courts to stay their executions at least long enough to establish with certainty that these new products wouldn't force them to suffer.
Chavez's latest appeals focused on the appeal of another death row inmate in Florida, Paul Howell, who got the state supreme court to order serious scrutiny of the new injection protocol before his scheduled February 26 execution.
But the US Supreme Court denied his final appeal without explanation, giving the green light to execute Chavez.