Millwall were one point above the relegation zone when Harris took over in February last season and he went on to steer them to 13th in the Championship.
They have won six of their 18 games so far this season and are six points off the play-off places, with defeat at home by Coventry on Saturday their first loss in 10 games – although they did not register a single shot on target.
They face Sheffield United at home on Wednesday in what will be Harris’ final time in The Den dugout, before the trip to the Riverside on Saturday.
A club statement said recruitment is already under way for Harris’ successor, with interim management plans to be announced after the weekend.
“A comprehensive recruitment process is already under way for a new head coach,” said director of football Steve Gallen.
“The direction we as a club want to head in is clear and the next head coach will play a pivotal role in helping us execute our strategy.”
