The relegation-threatened South Yorkshire side have not won since last July and are pointless in the Championship after 13 league defeats so far.
Cooke, 34, was named Championship Coach of the Year just seven months ago having led them to a highly creditable fourth place.
But this season has been a slog and the former Hull and Hull KR stand-off has left by mutual consent.
Assistant boss Chris Spurr has also left the Keepmoat Stadium with the club saying they are looking “to go in a new direction”.
Cooke initially joined as player-coach in 2012 after a year out of the sport following his last spell in Super League with Wakefield Trinity Wildcats.
He retired from playing last month and said yesterday: “I feel I owe these people and the club in particular a debt of gratitude which can never be repaid.
“It gave me a renewed lease of life, enjoyment after a very difficult period in my personal life.
“I feel deeply saddened and apologetic to everyone at Doncaster Rugby League Club, especially the fans for the 2015 season. I am certainly hurt by the club’s 2015 so far.”
Meanwhile, Sheffield Eagles look to close in on the top two tonight when they host Dewsbury Rams.
St Helens captain Jon Wilkin will go before disciplinary chiefs tonight faced with suspension after being accused of a reckless tackle on York winger Adam Dent.
Wakefield prop Mickael Simon has also been charged with a grade B offence of reckless striking with the shoulder on Leigh stand-off Martyn Ridyard.