Neil Warnock to leave Rotherham despite saving them from relegation
Warnock, 67, was appointed manager until the end of the season in February after Neil Redfearn was sacked.
The Millers were in the relegation zone when Warnock arrived but they finished in 21st place.
A club statement read: "We would like to place on record our thanks to Neil and his support staff for the 16 games that they led the team for."
Rotherham have held talks with Warnock over the past fortnight, but the former Sheffield United boss, along with assistant manager Kevin Blackwell and Ronnie Jepson have all departed.
The Millers won six and drew six of their 16 league games under Warnock - including an 11-game unbeaten run - which saw them finish nine points clear of the relegation zone.
The club have said they will appoint a new manager - their fourth in eight months - in due course.