It is the third national team job for the 34-year-old from Lisburn, who was Sierra Leone’s coach in 2013, at the age of 27, and also had a spell with Rwanda.
McKinstry had been coaching at Craig Bellamy’s academy in Sierra Leone for three years when he was asked to help the national team but he was sacked after 18 months.
His spell with Rwanda also lasted just over a year and he has since worked at clubs in Lithuania and Bangladesh.
”My objective will be to take the best of what is already there and combine it with both new talent and new working practices to improve performance,” McKinstry told a news conference in the Ugandan capital.
“With effort and application we can maximise both individual and team potential in the months and years ahead.”
In November, Uganda begin their bid to qualify for a third successive Africa Cup of Nations finals with their opening group matches away to Burkina Faso and at home to Malawi.