Woods will be honored on Monday 6th May.
At the ceremony the five times Masters victor received a standing ovation and President Trump said: "Congratulations again on your fantastic comeback and your wonderful life and for giving sports fans everywhere a lifetime of memories".
"The unbelievable Masters experience I just had a few weeks ago certainly is part of the highlights of what I've accomplished so far in my life on the golf course", he said.
Woods relationship with Trump dates back to before his presidency.
A presidential medal to a sports star usually wouldn't raise questions of conflicts.
Woods told the Rose Garden audience that his journey had been an "unbelievable experience".
Asked to say a few words, Tiger thanked his family and close associates for sticking by him through the "the highs and the lows".
Golfer Tiger Woods received the highest U.S. civilian decoration from President Donald Trump, prompting media and Democrats to brand him a Trump crony and dismiss his accomplishments in sports and life. Mr. Trump has golfed with Woods in the past, and has tweeted about him for years. The pair have been golf partners numerous times over the past decade, including a round with Nicklaus on February 2.
On Twitter, the President has been consistently supportive of Woods.More news: Buffett finally embraces Amazon as Berkshire acquires stake
Maintaining a friendship with this president has been tricky for some athletes, which New England Patriots quarterback Tom Brady discovered when a "Make America Great Again" hat was seen in his locker in September 2015. Trump has said he's lost billions of dollars since moving into the White House.
Some critics have blasted Woods over his links with Trump since the real estate mogul was elected president in November 2016. We've had dinner together.
"He's the President of the United States", Woods said. "No matter who is in the office, you may like, dislike personality or the politics, but we all must respect the office".
The Trump Organization has "repeatedly demonstrated their ability to successfully manage unique, high-end courses and golf clubs, and this is no exception", Woods said in a 2018 interview in the company's in-house magazine. Tiger wouldn't play the game - he is very smart. Trump had predicted over the winter that such a win was coming.
Trump spoke about Tiger's "strategic" shot-making and "clutch" putting. He was long, straight & putted fantastically well. Repeatedly, the man who can make fans roar on the final days of major tournaments seemed reflective, saying he has had to "battle" back to being an elite athlete. Not surprisingly, Jack also played really well.
After Monday's ceremony, Woods will continue readying for the second major of the season, next week's PGA Championship.
Woods took home the green jacket at the Masters in dramatic fashion in mid-April, earning his first major win in 11 years. "I don't mind telling you I'm really sore", he confessed immediately after that tournament.
Trump briefly alluded to Woods' career and personal downfall that includes his public divorce from wife Elin Nordegren and ensuing struggles on the course for years that preceded his comeback capped by last month's win at Augusta.