Sinclair, who is yet to confirm where his next post will be, joined Citizen from Burson-Marsteller in May 2013.
He will serve out his notice period and officially leave the company at the end of the year.
Citizen has undergone several management changes in the last 12 months, following the departure of its chief executive Frankie Cory in October 2013 for the same role at Mischief.
MD Misha Dhanak left Citizen in August this year but is also yet to announce her new role.
Sinclair said: "I'm incredibly proud of the unique creative culture we have fostered at Citizen. It's resulted in a passionate team, exciting clients and award-winning work. I'm now looking forward to a new challenge in the New Year."
Citizen will be announcing a new MD in the next few weeks.