The Armenian picked up an ankle injury during Tuesday's friendly with Luzern that will keep him out for a month, meaning he will miss his side's opening fixtures of the season
The Armenian playmaker joined the club earlier in July but the 24-year-old picked up a knock during Tuesday's friendly with Luzern in Switzerland.
"Borussia Dortmund have to make do without Henrikh Mkhitaryan in the coming weeks," a club statement read.
"According to team doctor Markus Braun he will probably be unavailable for up to four weeks."
The former Shakhtar Donetsk man will miss the DFL-Supercup fixture with Bayern Munich on July 27, their first round DFB-Pokal clash a week later and their Bundesliga season opener against Augsburg on August 10.
However, they hope he will be available for the first home league game against Eintracht Braunschweig on August 18.