Schaffer was appointed to fill a vacancy on the Colorado State Board of Education by a party vacancy committee, representing a district that is coterminous with the state's Fourth Congressional District. He successfully ran for the seat in 2006, against Democrat Tom Griggs. In January, 2009, Schaffer was made chairman of the Colorado State Board of Education with a unanimous decision of the four Republican and three Democratic board members. Fellow board members elected Schaffer to continue his chairmanship in 2011.