McKinlay, who joined Fulham in 2004, will continue his role at Craven Cottage, but will link up with new Northern Ireland boss Michael O'Neill during international breaks.
"I am honoured to accept the Assistant Manager's position with Northern Ireland," McKinlay said on Fulham's website.
"I have known Michael O'Neill for over 20 years since our days at Dundee United together and it will be great to work alongside him.
"I am excited by this opportunity to work with the squad as there are a lot of talented players from Northern Ireland and I am looking forward to our first game against Norway."
O'Neill won the race to succeed Nigel Worthington as Northern Ireland manager last December, but officially took up his new position last week.
The Irish Football Association later confirmed that former Shamrock coach and current St Johnstone assistant manager Tommy Wright has been appointed as O'Neill's goalkeeping coach.
The former Northern Ireland goalkeeper has, like McKinlay, taken up his role on a part-time basis and will spend most of the season with the Scottish Premier League club.
"Having represented my country as a player I am immensely proud to become the goalkeeping coach of the Northern Ireland senior squad," Wright told the Irish FA's website.
"Everyone knows that I'm very passionate about Northern Ireland and I am thrilled to be working alongside Michael O'Neill again. He is a fantastic young manager and I am sure he can inspire the players ahead of the World Cup Qualifiers in September."
O'Neill, whose first game in charge is a February 29 home friendly against Norway, is now confident that he has the backroom staff in place to help him put the country in a position to qualify for their first major international tournament since 1986.
He said: "I have known Billy and Tommy since my playing days and have watched as they both forged very successful careers in coaching.
"Both guys have tremendous reputations within football and that speaks volumes.
"Looking ahead, we are up against top-class opposition in our World Cup Qualifying group and I believe we have top class coaches in place which put us in the best position possible to compete against some of the best sides in the world."
McKinlay and Wright have both signed two-year contracts and will take up their positions on February 13.