The FA announced on Friday morning that Boothroyd had been appointed as a 'national coach'.
The 43-year-old will work across several youth groups, but his main focus will be with the Under-20s.
He will take over as full-time coach of that team following this summer's Toulon Tournament, for which Gareth Southgate will be in charge.
The former Northampton boss will also help the FA's coach education scheme.
On its website, the FA said: "The FA has appointed Aidy Boothroyd as a national coach.
"Boothroyd will report into England Under-21s head coach Gareth Southgate and the FA's director of elite development Dan Ashworth, taking up the role with immediate effect."
Boothroyd oversaw Watford's promotion to the Barclays Premier League in 2006 and also guided the Hornets to the FA Cup semi-finals the following year.
Boothroyd had spells at Colchester, Coventry and Northampton after he left Vicarage Road in 2008.
Northampton sacked Boothroyd in December after he had spent two years at the Sky Bet League Two club. At the time of his dismissal, Northampton were bottom of the Football League.
Boothroyd said of his FA role: "I'm excited by this opportunity. Youth development is where it all began for me and I have taken on aspects of that into my management - that love of coaching and developing players has kept going.
"At Watford I helped bring through players like Ashley Young and Ben Foster early in their careers, and more recently, I had Saido Berahino when I was Northampton Town manager. I have always wanted to bring young players through."