The 36-year-old reserve team coach will take charge of the side for the forthcoming away game at Swansea City this coming weekend.
Mackay will be assisted by current first-team coach Martin Hunter and Sean Dyche.
Boothroyd left Watford by mutual consent on Monday evening as the club slumped to 21st in the Championship table after the 4-3 home defeat to Blackpool last weekend.