Trump's endorsement comes as Moore, 70, faces allegations from at least eight women in recent weeks who have accused him of sexual misconduct or inappropriate behavior toward them when he was in his 30s and, in some cases, the women were in their teens.
He has denied the allegations.
The two men spoke over the phone this morning, with Trump expressing "enthusiastic support for Judge Moore's candidacy" according to a statement released by the campaign after the call.
Moore tweeted that he was "honored" to receive the endorsement and said Trump told him, "Go get 'em, Roy!"
"The president had a positive call with Judge Roy Moore, during which they discussed the state of the Alabama Senate race, and the president endorsed Judge Moore's campaign," White House deputy press secretary Raj Shah said in a statement.
Trump has no plans to campaign for Moore, but he will be holding a rally in Pensacola, Florida, on Friday, less than 30 miles from the Alabama state line.
Trump defended Moore last month against the allegations of sexual misconduct, telling reporters before departing for the Thanksgiving holiday, "Let me just tell you, Roy Moore denies it. That's all I can say. He denies it. By the way, he totally denies it."
While many Republicans called on Moore to drop out in the immediate wake of the allegations, the calls for him to step aside have quieted in recent days.
Moore faces Democrat Doug Jones in the election, which will be held Dec. 12.