Mr Hooper has officiated 42 games so far this season, mainly in the Championship.
His most recent match in charge came last Sunday on the final day of the Championship season when Reading defeated hosts Burton Albion 4-2 at the Pirelli Stadium.
The match official's last game in the middle involving City came back in January 2016 when the Bantams lost 1-0 at home to Barnsley.
The ref has recent experience of officiating in a play-off final after taking charge of the 2015 League Two final between Southend United and Wycombe Wanderers.
Mr Hooper will be joined by assistant referees Nick Hopton and Neil Davies for the City's final with Millwall later this month, while Nick Greenhalgh has been designated as the reserve assistant referee.
Chris Kavanagh will be the fourth official.
Meanwhile, it has also been confirmed that City will wear their home strip of claret and amber shirts, black shorts and black socks for the final.
Opponents Millwall will wear navy and white shirts, white shorts and white socks at Wembley.