Jones has a 45-year career in law enforcement and was the Shawnee County sheriff before Kelly appointed him patrol superintendent in 2019.
Several women, all current and former patrol employees, sued top agency officials in federal court in 2021, alleging discrimination and a hostile work environment. Two former majors sued in 2020, alleging they were dismissed for helping women lodge complaints against top officials.
Kansas Highway Patrol Superintendent Herman Jones and Adjutant General David Weishar will both leave office this year.
Kelly told the Topeka Capitol-Journal in December that two independent investigations found no substance to the allegations made against Jones.
VERMONT SHERIFF TAKES OFFICE WHILE FACING TWO INVESTIGATIONS
Some Republican lawmakers have suggested putting the patrol under the direction of the Kansas Attorney General's office if Jones was not removed.
Kelly did not name a replacement for Jones.
Weishaar was appointed the Adjutant General on April 1, 2020. Kelly named Brig. Gen. Michael Venerdi to replace Weishaar. He currently has leadership roles with the Kansas Guard and previously was commander of the 184th Wing at McConnell Air Force Base.