McOnie will join choreographer Ruth Brill for an interim artistic team that will oversee the company’s 2019 season.
Smillie, who becomes artistic director in 2016, said: “I feel hugely privileged to have led this extraordinary company of young creative talent. I’m proud of all we have achieved together and look forward to seeing the company’s unique artistic vision fly in the many years to come.”
The trustees of the organisation said Smillie had led the organisation “through a challenging period of transition, put firm foundations in place for its future development, and departs with our heartfelt thanks and appreciation for her massive contribution to our success”.
The company said it was seeking to recruit a new artistic director to deliver its “next chapter”.