The decision to end ties with the Northern Irish tactician comes just two days after rumours went round in Uganda.
The 35-year-old failed to qualify the Cranes to a third successive Africa Cup of Nations finals in Cameroon and this saw him fired.
Fufa has confirmed the latest development by stating on their official website.
“The head coach of the Uganda men’s national team, Johnathan McKinstry, has today (Monday) reached an agreement with Fufa to bring an end to his 18 months at the helm of the Uganda Cranes.”
“Fufa would like to thank coach McKinstry and his staff for the work and dedication to developing the Uganda Cranes during their tenure.”
“Coach McKinstry departs Uganda having won two in every three games played, recording a 67% WIN rate from the 18 games he has overseen – including 12 wins, three draws, and only three defeats.”
“In addition to this, Coach McKinstry guided Uganda to victory in the Cecafa Senior Challenge Cup 2019 where Uganda won all of the games contested, for only the second time in their history.”
“We would like to thank Coach McKinstry for the professionalism demonstrated during his employment with Fufa, and we wish him well in all his future endeavours.”
McKinstry’s problems with FUFA started after losing to South Sudan in Nairobi.
The loss ultimately changed Uganda’s 2021 Afcon qualifying trajectory.
It should be noted that ahead of the Afcon home qualifier against Burkina Faso, Fufa announced they had asked McKinstry to step aside.
They tasked his then assistant Abdallah Mubiru to oversee it and the final match away to Malawi.