The price increase will be between 3% and 5%, CEO Steve Ells said on the company's conference call yesterday.
Chipotle's chicken burrito currently costs $7.81 in New York. A 5% increase would raise the price to about $8.20.
Ells said that the company is going to start charging more as it eliminates Genetically Modified Organisms from its ingredients.
Activists have said that GMOs might not be as safe as natural foods because they have been altered from their natural states.
Ells said he hopes to time Chipotle's price increase around the elimination of GMOs.
"We are not aware of any other restaurant company anywhere near our sight that's even attempting to do this and so to actually accomplish it will be pretty exciting and we'd like to time that excitement around with the price increase," Ells said.