Champion, 52, has been on "Good Morning America" since 2006. He had previously worked at ABC-owned local New York station WABC-TV since 1988. He has broadcast more than 1,800 weather forecasts and has traveled to nearly every major national weather event.
"While he is leaving ABC News, he will always be a part of our family," said ABC News President Ben Sherwood.
His last day on the morning news show will be Wednesday.
"Only an amazing opportunity like this ... could take me away from my ABC family," Champion tweeted.
At the Weather Channel, Champion will anchor the network's new flagship morning show, which is set to debut in early 2014, and he will also assume managing editor responsibilities.
Ginger Zee will take over weather responsibilities at "GMA" and across the news division. Zee became weather anchor for the weekend edition of "GMA" two years ago.
The Associated Press contributed to this report.