Manager Owen Coyle has the option to make the 19-year-old winger's move permanent at the end of the campaign.
Guerrero then impressed as a trialist during Burnley's pre-season tour of America in July.
Coyle said: "Fernando is an exciting player for just 19 years of age and we believe he has unbelievable potential.
"We have agreed a loan deal, subject to an option to buy him.
"Obviously he is valued very highly by his club in Ecuador and if he comes in and shows us the quality we know he possesses I think he can go on to become a truly outstanding player."