[5] McKinstry has coached in several countries; Northern Ireland, England, USA, Ghana, Sierra Leone, Rwanda, Lithuania, Bangladesh and Uganda.

His early career was focused on elite youth development through roles with Newcastle United, New York Red Bulls, the Right to Dream Academy and the Craig Bellamy Foundation.

[5] McKinstry spoke about his desire to be awarded the job on a permanent basis[12] and was subsequently retained as head coach for the 2015 CAF Nations Cup qualifiers.

Following defeats to Ivory Coast and DR Congo during a period when Sierra Leone were banned from playing fixtures at home because of the Ebola outbreak, he was sacked in September 2014.

[16] In his first competitive game in charge, McKinstry guided Rwanda to their first away win in four years with a 1–0 victory over Mozambique in the opening round of 2017 African Nations Cup qualifying.

[18][19] In January 2016, McKinstry led Rwanda to the knock-out stages of a major competition for the first time in their history[20] when he guided them to 1st place in Group A of the 2016 edition of the CAF African Nations Championship[21] and qualification for the Quarter Finals.

[24] Shortly after the extension of McKinstry's contract, Rwanda recorded their biggest ever win in the Africa Cup of Nations when they defeated Mauritius 5–0 in Kigali.

He cited the ongoing uncertainty regarding Kauno Žalgiris' league status[28] as a key factor in the decision between himself and the club to go their separate ways.

[29] On 7 November 2018, McKinstry was named as the new head coach of Bangladesh Premier League side Saif SC, replacing Englishman Stewart Hall.

[41] Despite these challenges, his first season at the club would end in success - guiding Gor Mahia to win the Kenyan Premier League title.

Leading Gor Mahia to win the 2023-24 FKF Charity Shield[43] and the 2023-24 Kenyan Premier League with an 8 point margin over their nearest rivals.