McKinstry has already started plans to help the team have a good 2022 World Cup qualifying campaign.
McKinstry returns after Uganda Cranes failed to secure an Africa Cup of Nations ticket to Cameroon.
“A busy day following up with Uganda Cranes players after their return to their clubs,” McKinstry tweeted.
The tweet was accompanied with a picture of him tracking the players, who ply trade in different teams.
“Planning is already underway for the start of our Fifa World Cup campaign in June when we will kick off our journey to Qatar,” he added.
The Northern Irish coach was suspended for the team’s last two Afcon Group B qualifiers against Burkina Faso and Malawi.
This came after Cranes’ poor performance in the African Nations Championship.
The East Africans were crashed out before the knock-out stage.
Questions have been raised over the future of the 35-year-old however, Fufa has been silent.
But after a recent tweet by the youthful tactician is, it seems the two parties have decided to continue working together.
McKinstry’s charges will start their campaign away to Kenya in June, before playing Mali at home in the same month.