Jason Done, who played the schoolteacher, has already filmed his final scenes after seven years in the role.
Tom will feature in the next block of ten episodes, which are due to air later in the spring, and show chiefs are promising a memorable exit for the fan favourite.
Waterloo Road's executive producer Cameron Roach told Digital Spy today: "We will be sorry to see Tom Clarkson leave Waterloo Road, but we promise a finale that can't be missed, in order that we send this much-loved character off in style.
"We wish Jason all the best for the future and thank him wholeheartedly for the energy and commitment he has given the role. He has been a big part of the Waterloo Road story."
Done added: "A massive thank you to everyone who's been involved in the making of Waterloo Road. I'm very proud of what we have achieved and the laughter we have shared."
Meanwhile, Alec Newman and Daniela Denby-Ashe have also left their respective roles as headteacher Michael Byrne and businesswoman Lorraine Donnegan.
Brian Park, managing director of Waterloo Road's production company Shed Productions, told Digital Spy: "Jason, Alec and Daniela all feature significantly in the next series and their departures will have all Waterloo Roaders on the edge of their seats."
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