The reward is a deserved accolade for the 26-year-old, outstanding during the Reds' outstanding upturn under Valerien Ismael, which has culminated in them clinching a play-off spot at second-tier level for the first time since 1999-2000.
It is the second time that Doncaster-born Mowatt has been named in a yearly line-up by his peers. He earned a place in the League One side in 2018-19 following Barnsley's promotion back to the Championship.
This year's Championship line-up, announced in an awards ceremony on Sky Sports, is dominated by Norwich City players with Max Aarons, Grant Hanley, Emi Buendia - named as the division's player of the year - and Teemu Pukki all named in the side, with Daniel Farke named as the manager.
Bournemouth players Asmir Begovic and Arnaut Danjuma Groeneveld also feature in the side along with Reading's Michael Olise, Brentford hot-shot Ivan Toney, Cardiff captain Sean Morrison and Watford defender Adam Masina.
Meanwhile Hull City duo George Honeyman and Callum Elder has been named in the League One yearly line-up by their fellow professionals, while head coach Grant McCann has been named as the best manager.
Honeyman was pipped to the League One player of the year award by Peterborough United's Jonson Clarke Harris.
Meanwhile, Bradford City striker Lee Novak beat off competition from the likes of Mowatt and Huddersfield Town forward Fraizer Campbell to win the 2020 Mitre Goal of the Season - for his spectacular overhead kick in the Bantams League Two win at Grimsby Town just before Christmas.
Doncaster Rovers midfielder James Coppinger, who will retire in the summer, claimed the prestigious Sir Tom Finney award.