The Dragons had already been on the longest losing streak in club history before Saturday's 30-12 loss to South Sydney made it 11 defeats in a row.
Club powerbrokers had been deliberating the decision before moving on Monday morning, with players and staff informed soon after Flanagan.
His axing comes less than nine months after the Dragons tied the 2016 premiership-winning coach to a new two-year contract extension.
The Dragons won only one game after the extension was announced; his new contract had been set to begin in 2027.
Dragons chair Andrew Lancaster and chief executive Tim Watsford confirmed at a snap press conference on Monday that Flanagan had left his post "by way of mutual agreement".
Lancaster claimed Flanagan had not been fired.
The Dragons have also parted ways with general manager of football Ben Haran, who had presided over the club's underachieving playing list.
"The decision followed discussions between Shane, Ben and club leadership and all parties agree the time is right for a new direction," Watsford said.
"These are not decisions anyone takes lightly.
"This is clearly a significant moment for the club. We understand the disappointment and frustration our members and fans feel. We know that results and performances have not met expectations."
The club's board will meet on Tuesday and decide on an interim coach to take charge of the Dragons, who have now fired three full-time coaches since last playing finals in 2018.
Assistant coach and 2010 premiership player Dean Young appears a strong candidate, having long been earmarked as a head coach in waiting.
He took over mid-season when the Dragons fired Paul McGregor in 2020, and also held the interim role at North Queensland before Todd Payten was appointed.
Michael Ennis, another of Flanagan's former assistants, is also an option but is untested as an NRL head coach.
Young and his former Dragons teammate Ben Hornby, an assistant at South Sydney, are both considered chances to take on the role full-time next year.
The interim coach's first game will be the Dragons' most important game of the regular season, the traditional Anzac Day clash with the Sydney Roosters.
Flanagan leaves with a 35 per cent win rate, claiming 19 victories from 55 games since taking over for the 2024 season.Â
22°C