Clive Platt and Ishmel Demontagnac were handed surprise starts at Wembley but were left to watch in horror as the Bantams raced into a three-goal lead.
Boothroyd, to be fair, could not have planned for his side to freeze in such a big game and said afterwards he had no regrets about his team selection.
“I wouldn’t do anything differently," was his verdict.
"As a manager you have a plan for what you’ve got to do.
“If you pick a team and it wins then you’re a very good manager and if they don’t win then things are always said. That’s why football is such a game of opinions.”
The morning of the game saw Boothroyd featured heavily in the national press as it appeared he was on the verge of re-emerging as a manager with the potential to reach the very top of the game.
His Northampton future will now be questioned after reported interest from other clubs but the scale of the defeat at Wembley may make him more determined to achieve promotion with Town next season.
How quickly managerial fortunes can change on a weekend when Gary Johnson, who struggled to make any sort of impact at Sixfields, could be back in the Championship with Yeovil.