The protesters demanded that the US take action to stop further spread of the film through internet.
Eyewitnesses said the demonstrators stretched kilometres through the city, shouting anti-American and anti-Israeli slogans.
A pro-Iranian group, Islamic Movement of Nigeria, that identifies with Shiite Muslims, organised the demonstration after holding a similar rally a few days ago in another northern city of Zaria.
They marched to the palace of the Emir of Kano, carrying pictures of US President Barack Obama.
Some demonstrators also waved Iranian flags.
Nigerian protests have so far remained peaceful.