Faria announced earlier this month that he was to leave the club after spending 17 years working under Mourinho.
Mourinho said after Farias announcement that the Portuguese was irreplaceable and he would instead look at filling the gap by using Michael Carrick and other members of his backroom staff.
According to Duncan Castles, Mourinho has now promoted highly successful U18 coach McKenna and he will work alongside Carrick and incoming Sampdoria fitness coach Stefano Rapetti.
McKenna joined United from Tottenham in 2016 and has enjoyed two successful terms as coach of the U18s.
He guided the side to the North title last term and is noted for his attacking playing style that involved the likes of Tahith Chong and Angel Gomes.
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Faria quit United in order to spend more time with his family but the Portuguese is expected to be on the lookout for managerial roles after some time off from football.
United ended the season trophyless after their defeat to Chelsea in the FA Cup final and Mourinho could have done without a summer of upheavel behind the scenes as he targets a title tilt next term.