Mkhitaryan was one of AS Roma’s best players last season as they finished seventh on the Serie A table and reached the semi-finals of the Europa League under Paulo Fonseca.
The former Borussia Dortmund midfielder joined Roma initially from Arsenal in the summer of 2019 before signing permanently the following season.
His contract was due to expire this summer but he will now work under Jose Mourinho, who managed him at Manchester United, next season.
Mkhitaryan made 46 appearances in all competitions for Roma last season and scored 15 goals; 13 of those in the Italian Serie A.
After signing his extension, Mkhitaryan said: “Over the last two years at Roma I’ve fallen in love, both with the club and the city, thanks in large part to the incredible passion of the fans.
“The club’s ambitions are very high and I am proud to have the chance to play my part as we take on all the challenges that await us next season. Daje Roma!”
General manager Tiago Pinto added: “We are very pleased that Henrikh has decided to continue his adventure with Roma.
“As he has already shown with his performances on the pitch, his quality will be very important in helping the team reach their targets next season.”