Carroll, 56, was put to death by lethal injection at Florida State Prison in Starke, the Orlando Sentinel reported.
Carroll did not make a final statement, prison officials said.
His victim's mother, Julie McGowen, formerly known as Julie Rank, said: "Thank you to all that have worked so hard, and justice for all, namely, Christine McGowen. Rest in peace."
Julie McGowen was at work and Christine's stepfather was asleep when Carroll raped and strangled the 10-year-old in her bed Oct. 30, 1990.
Carroll had been released from prison and was staying in a halfway house next door to his victim's home in Orange County.
The Catholic Diocese of Orlando held a service just before Carroll's execution, praying for abolition of the death penalty, the newspaper said.
"It's a destructive tool rather than a preventive tool," Bishop John Noonan said at the service.
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