"Luther Strange has been shooting up in the Alabama polls since my endorsement," Mr Trump wrote in one now-removed post.
He campaigned for Mr Strange, but could not save him from defeat to ultraconservative firebrand Roy Moore.
The underdog's victory has sent shockwaves through Washington.
Things Republican Roy Moore believes
In one now-deleted Tweet, the president said Mr Strange "will never let you down!" according to news website ProPublica, which documents Mr Trump's posts.
In another, the president said "vote today for 'Big Luther'".