The 43-year-old Farmer appeared Thursday before U.S. Magistrate Judge Robert Wier in Lexington for a brief arraignment hearing.
His attorney, Guthrie True, entered the plea for him.
Farmer will be free until his trial, set for July 2.
Farmer is a state basketball icon whose jersey hangs from the rafters of Rupp Arena. He was charged in an indictment earlier this week with four counts of misappropriating government property and money and one count of soliciting property in exchange for a government grant.
Farmer served as agriculture commissioner from 2004 through 2011. He could face up to 10 years in prison and a $250,000 fine on each of the five counts.