The Professional Footballers' Association, an organization made up of professional players in England, voted for the Australian midfielder to be included in a midfield four along with Fulham's Tom Cairney, Brighton's Anthony Knockaert and Newcastle's Jonjo Shelvey.
Mooy, who has played in a predominately deep midfield role for the majority of the season has played 41 matches in the Championship, scoring four goals and setting up six more.
The former Melbourne City midfielder joined Manchester City in July 2016 before being loaned to Huddersfield Town.
Huddersfield are currently in fourth position and on target to take part in the promotion play-offs that could see them move up to the Premier League.
Mooy has been instrumental in Town's rise - from narrowly avoiding relegation last season, finishing 19th, to being one of the favourites for promotion.
The 26-year-old has been linked to numerous Premier League clubs, with Manchester City's Pep Guardiola also interested in taking a look at Mooy before deciding his future next season.
Mooy is averaging the second most amount of passes per match (71) in the Championship, only behind Fulham midfielder Cairney. The Aussie is also tenth in the Championship when it comes to chances created per-match (2.1).
Huddersfield boss David Wagner has sung Mooy's praises calling him the Championship's signing of the season.
And after Mooy starred in the Yorkshire club's 3-0 win over Norwich two weeks ago Wagner hailed his contribution.
“Every manager is happy when you have a player who is a little bit variable and who is able to play different positions,” said the highly-rated German coach.
“But I still believe Aaron Mooy is an extra class number eight and a good number ten as well."
PFA Championship Team of the Season
Goalkeeper - David Stockdale (Brighton & Hove Albion)
Defender - Bruno Saltor (Brighton & Hove Albion)
Defender - Lewis Dunk (Brighton & Hove Albion)
Defender - Jamaal Lascelles (Newcastle United)
Defender - Ryan Sessegnon (Fulham)
Midfielder - Tom Cairney (Fulham)
Midfielder - Anthony Knockaert (Brighton & Hove Albion)
Midfielder - Aaron Mooy (Huddersfield Town)
Midfielder - Jonjo Shelvey (Newcastle United)
Forward - Dwight Gayle (Newcastle United)
Forward - Chris Wood (Leeds United)