The Arsenal midfielder has been on loan at the Stadio Olimpico this season.
"I'm very pleased," Mkhitaryan told Roma's website.
"I'm happy to extend my stay here, because I still have things that I haven't achieved yet that I want to achieve.
"I'm looking forward to it."
Roma chief executive Guido Fienga added: "We are happy that Henrikh has decided to stay with us, and help us continue to grow.
"The club's targets have not changed and we always want to have players at our club, like Micki, who show their desire, professionalism and determination, who represent our club and our fans in the right way.
"I hope Micki stays at Roma for a long time - and I want to congratulate him on the birth of his son here, too."