Played by Noah Wyle, Carter's character will say goodbye to coworkers at the city's County General Hospital in the May 19 season finale.
The network recently agreed to renew the 11-year-old series for two more years. Carter will return for four episodes in each of the next two seasons, producers said.
"It's very sad for me. Noah and I have a lot of history together," said executive producer John Wells. "He's a wonderful actor and a wonderful man, and it's been great to watch him grow up and get married and have a family."
Wyle, who has been with the show from the beginning, received five Emmy nominations for his portrayal of Carter.
'SNL': 'Anchorman 2' cast, One Direction sing 'Afternoon Delight' [VIDEO]
Wisconsin business offering 'therapeutic cuddling' forced to close