The Usual Suspects director said he was disappointed to leave the film, which he described as "a passion project".
The Queen biopic, Bohemian Rhapsody, has a new director.
The studio statement on Fletcher's hiring doesn't indicate whether or not there'll be reshoots or if he'll be drastically changing the make-up of Singer's film, but it's likely that there'll be a number of scenes reshot as Fox claims that Singer was regularly absent from the set.
Filming is scheduled to resume next week in London.
Fletcher, primarily known for his roles in Band Of Brothers, Lock Stock And Two Smoking Barrels and Layer Cake, previously directed the English crime thriller Wild Bill and the sports comedy biopic Eddie The Eagle, starring Hugh Jackman and Taron Egerton.
The film has gone through a lot of snags throughout its years-long development, and for several months between 2013 and 2014, Fletcher was one of the rumored directors attached.
Singer denied speculation his exit was down to "a dispute" with lead star Malek - who will play the band's late frontman Mercury in the motion picture - but admitted they did have "creative differences" on set at times. That means Bohemian Rhapsody will hit theaters on December 25, 2018, as planned.
Fletcher joins the production after Singer was sacked on Monday after he failed to show up to set on multiple occasions. Yet Singer claimed in a statement to The Hollywood Reporter that he was sacked because Fox would not let him take care of a "gravely ill parent".
He added: 'Rami and I successfully put those differences behind us and continued to work on the film together until just prior to Thanksgiving'. Lucy Boynton also stars as Mary Austin, Mercury's muse and lover.