He argues they are illegal and counterproductive and earlier this month he led thousands of supporters -- and a group of American peace activists -- on a march to the edge of the restive tribal districts to protest against drones.
On Twitter, Khan said he was stopped by US officials in Toronto.
"I was taken off from plane and interrogated by US Immigration in Canada on my views on drones. My stance is known. Drone attacks must stop," he wrote.
Khan said the delay meant he missed his flight and a party fundraising lunch in New York, but insisted "nothing will change my stance".
PTI spokesman Shafqat Mahmood criticised the move.
"PTI strongly condemns the off loading of Imran Khan at Toronto airport and questioning on principled stand against drones. US shd apologise," he wrote on Twitter.
US officials in Washington declined to comment.