McGowan is charged with first degree murder, two counts of aggravated assault on a law enforcement officer, aggravated endangering of a child, fleeing law enforcement and criminal possession of a firearm.
Authorities are still waiting to determine if McGowan will face kidnapping charges.
Leavenworth police say McGowan kidnapped 5-year-old Cadence Harris from Atchison on Friday.
Her body was found in McGowan's car after a shootout with police in Leavenworth.
Police still have not revealed any details about how Cadence died.
McGowan is the boyfriend of Cadence's mother.
McGowan is being held on a $1 million bond.