Place oil in a saucepan over medium heat. Heat oil to 250 degrees F (120 degrees C) using a candy thermometer to gauge temperature.
Break chipotle chiles into small pieces and place into a a spice grinder; pulse to grind into 1/8-inch pieces. Stir ground chipotle chiles and red pepper flakes into the hot oil. Cook until chile oil begins to foam, 3 to 5 minutes.
Remove chile oil from heat; cover and let sit for 4 hours to overnight. Pour chile oil through a fine mesh strainer into a sealable container.