Bush, his father — former President George H.W. Bush — and 2012 Republican nominee Mitt Romney did not support Trump, an unusual move for top GOP figures.
George W. Bush and his wife, however, did vote for down-ballot candidates, according to reports.
Reports had suggested both presidents Bush could vote for Clinton, though it was not immediately known for whom the elder bush cast his ballot.
Trump, who ran on a pledge to shake up an entrenched Washington, has at times worn the lack of support from so-called "establishment" figures as a badge of honor.
Trump defeated the younger Bush's brother, Jeb, in the GOP primary.