The producer will play an exclusive set at the Manchester event on December 6.
"He's not on tour and wasn't scheduled to be landing in the UK at all this winter, but he wants to come and put the new venue through its paces," organisers said.
"He's going to be picking out the rest of the lineup so stand by for that."
This year's Warehouse Project kicks off on September 28 and runs for 12 weeks until New Year's Day.
Last year, organisers confirmed a change of venue for the event but announced it would remain in Manchester despite rumours of a move to London.
Tickets for the Skrillex show are priced at £18.50 and go on sale this Friday (August 31) at 9am.
Watch the Skrillex 'Bangarang' video below: