Health officials say the city ran out sooner than anticipated.
Dr. Brendan Hanley, Yukon's Chief Medical Officer of Health, says there's no word yet on when the territory will receive more vaccine.
He says anyone who received the flu shot since 2009, or who has had H1N1 before, will be at least partially protected.
Hanley says he will not restrict who can have access to a flu shot when more vaccine arrives.
On Friday, N.W.T. and Saskatchewan began restricting access to flu shots to people at high risk as their supplies of vaccine ran low.