Hetherington is being held to account for comments he made concerning the RFL's investigation into alleged homophobic remarks by Rhinos full-back Zak Hardaker, when he accused the governing body of carrying out a witch-hunt against the 22-year-old and called for an external probe.
Hardaker was last week cleared due to a lack of evidence, but now it is Hetherington who has drawn the RFL's ire and will go before an independent tribunal a week on Wednesday.
An RFL statement read: "Leeds Rhinos Chief Executive Gary Hetherington has been charged with Improper Conduct for questioning the motivation and integrity of an RFL investigation into an incident in his club's First Utility Super League fixture against St Helens played on Friday August 29.
"Mr Hetherington is charged with a breach of Operational Rule D1.8 (c) (Improper Conduct) by engaging in conduct which is prejudicial to the interests of the game.
"The charge will be heard by an independent Operational Rules tribunal on Wednesday October 1."
Hetherington took on the role of chief executive at Leeds in 1996 and has overseen a period in which the club has won six Super League titles in the last decade.