"We are saddened to confirm that Sam Kendricks tested positive for Covid-19 and will not compete in the Olympic Games Tokyo 2020," the USOPC said in a statement on Twitter.
Kendricks won back-to-back gold medals at the 2017 and 2019 world championships and was one of the main contenders for the title in Tokyo along with Swedish world record holder Armand Duplantis.
The charismatic 28-year-old, a bronze medallist at the 2016 Rio Olympics, is now in isolation, the USOPC added.
"In alignment with local rules and protocols, he has been transferred to a hotel to be placed in isolation and is being supported by the USATF (USA Track and Field) and USOPC staff," the USOPC said.
"Sam is an incredible and accomplished member of Team USA and his presence will be missed. Out of respect for his privacy, we cannot provide more information at this time."
The positive test comes just two days before the start of the men's pole vault competition on Saturday.
Kendricks' father and coach, Scott Kendricks, had first announced news of his son's Covid test result earlier
Thursday in an Instagram post that was subsequently deleted.
"Today in Tokyo officials informed Sam that his daily test for Cov 19 was positive," Scott Kendricks wrote. "So he is out of the competition. He feels fine and has no symptoms. Love you son. See you soon."