This will be the 38-year-old's first game officiating in the top-flight this term as Steve Bruce's side take on José Mourinho's side at the Tottenham Hotspur Stadium.
Although Bankes was the VAR for the Magpies' opening day win at West Ham United, the last time he refereed a game involving Newcastle came in a 1-0 defeat at Crystal Palace back in February, with former loanee Valentino Lazaro receiving a straight red card in stoppage -time.
Bankes also booked six United players at Selhurst Park that day, including Matt Ritchie, Jamaal Lascelles, Miguel Almirón, Sean Longstaff, Nabil Bentaleb and Joelinton.
The Englishman was also the referee for the FA Cup fourth round replay win at Oxford United as well as the 1-1 draw at Wolverhampton Wanderers in January.
Despite only officiating two games so far this season, Bankes has already handed out a red card, sending off Wycombe Wanderers' Darius Charles in the Chairboys' 5-0 defeat to Blackburn Rovers in the Championship.
On Sunday, Bankes will be assisted by Peter Kirkup and James Mainwaring, while Mike Dean will be the fourth official. Lee Mason will be in charge of VAR and is to be assisted by Andy Halliday.