The Belgium global striker, who is now on loan in Germany from Premier League side Chelsea, suffered ankle damage during a Ruhr derby date with Schalke on Sunday.
A Dortmund club tweet said: "Michy Batshuayi has sustained an ankle injury in the derby against Schalke".
For now, Batshuayi will likely be heading back to Chelsea's training facility in Cobham starting the rehabilitation process. However, he could still recover in time for the FIFA World Cup in Russian Federation.
Batshuayi, 24, has enjoyed a new lease of life since joining BVB from Chelsea on loan in January.
"Well its not good news for now, my season is probably over, and i wont be able to pay BVB back for their confidence", the Belgium worldwide posted via his official Twitter account.
Dortmund's statement confirming Batshuayi's injury said it was "in the realm of possibility" he could recover in time for the World Cup.
"I won't be able to pay BVB back for their confidence - thank you all the awesome amount of love I received since yesterday".
Batshuayi is playing on loan at Borussia Dortmund where he has lit up the Signal Iduna Park, netting seven times in 9 appearances.