The 26-year-old joined Dortmund from Shakhtar Donetsk in July 2013 and has since developed into an important first-team member at the club.
However, he has grown unhappy with life at Signal Iduna Park, with Dortmund scrapping against relegation and the future of a number of stars shrouded in doubt.
The attacking midfielder has been linked with Juventus in recent months and Raiola admits he is ready to explore Mkhitaryan's options.
"Henrikh wants to leave Dortmund at the end of the season," Raiola was quoted as saying by Bild.
"We will have to wait and see what we can do."
The midfielder has scored twice in 21 appearances in all competitions so far this term.
Mkhitaryan has a contract with Dortmund until June 2017, but the Bundesliga outfit could be tempted to cash in on the Armenia star if they can recoup a large part of the €27.5 million they paid for him in 2013.