Atkinson will also be assisted by an English team for the game, which takes place in the Polish national stadium in Warsaw.
Mike Mullarkey and Stephen Child will be Atkinson’s assistant referees, with Anthony Taylor and Andre Marriner acting as additional assistant referees and Jake Collin is appointed as reserve assistant referee.
"I am very honoured to be appointed to this important UEFA final and proud to represent The FA and my colleagues, not just in the Select Group, but English referees as a whole," said Atkinson, who admitted he was surprised and delighted to learn of his appointment.
"I would like to thank my family, friends, colleagues and finally my team for their support in helping me to achieve this dream appointment. It’s a very proud moment in my career."
It rounds off an impressive season for the Yorkshire-based official, who has taken charge of some top-level UEFA matches this term in addition to his regular Premier League and FA Cup involvement.
Recently, Atkinson refereed the Champions League semi-final first leg between Juventus and Real Madrid after previously officiating the quarter final tie between Bayern Munich and FC Porto.
He was also commended for his handling of a drone incident in the Euro Qualifier between Serbia and Albania in Belgrade last October, which led to the match being abandoned.
“His hard work, skill, diplomacy and humility have been justly recognised and rewarded”
And David Elleray, Chairman of The FA Referees’ Committee and member of the UEFA Referees' Committee, shared his approval of the appointment.
"I am sure that everyone joins me in congratulating Martin and his team on their appointment to this prestigious final," said Elleray.
"Martin and his team of officials have work to the highest level all season and have won praise not just for the quality of their officiating but also then immaculate way they handled events in Serbia when Martin’s calmness was a key factor in preventing an ugly situation escalating.
"Without doubt, Martin has been a most consistent international performer and he has been supported by a very experienced and focused team.
"His hard work, skill, diplomacy and humility have been justly recognised and rewarded.
"This honour adds to recent appointment of English officials to the UEFA Champions League final, UEFA Super Cup, Women’s EURO final, FIFA World Cup final, Olympic final, and Futsal FIFA World Cup final demonstrating the outstanding and unrivalled achievements of English international match officials."