Former Olympian Jenner will now be known as Caitlyn.
"It takes courage to share your story," Obama tweeted in response to Jenner's first tweet as Caitlyn.
"Your story matters in the fight for LGBT rights," he added.
The 65-year-old reality TV star's new Twitter page, in the name of Caitlyn, has beaten the President's record for the fastest growing micro-blogging account of all time.
Within his first hour on the Twitter site, Jenner attracted 280,000 followers.