A statement from the club has confirmed that Magilton and his assistant John Gorman have left Rangers 'by mutual consent'.
Magilton's departure come's after the club had suspended him for an alleged confrontation with midfielder Akos Buzsaky after the 3-1 defeat to Watford at Vicarage Road earlier this month.
"The club can confirm that Jim Magilton and John Gorman have left Queens Park Rangers by mutual consent," the club statement read.
"Recent events have been widely reported and whilst Jim Magilton completely denies the allegations, with the full support of John Gorman, it has been agreed that it is in the best interests of the club and Jim Magilton, if the parties move on in their separate ways.
"The club would like to wish both Jim Magilton and John Gorman good luck in the future and thank them for their hard work."