Embleton leaves with the Club in 14th position in the table and following a run of seven games without a win and only four wins in its last 15 matches.
Orient Chairman Nigel Travis said: “This was an extremely difficult decision for us to make, and one which we have done with heavy hearts.
“Nobody can underestimate, nor should ever forget, the influence and impact Ross has had on the rebirth of our Club. He was an integral part of our National League success and he stood up to lead the team following the tragic loss of Justin Edinburgh, and again put himself forward when we were later in need of a Head Coach.
“He is a bright young coach with a strong philosophy and some excellent ideas, but the board felt that with the investment made in the squad and the current situation in football that we should be looking to push on at an accelerated rate and unfortunately in recent weeks that has not happened.
“I’m confident Ross will bounce back from this as he has a lot to offer a club and we genuinely wish him every success in the future and thank him for all he has done for us.”
Embleton, 39, first worked for Orient between 2000 and 2009, and was in charge of the Club’s then Centre of Excellence before leaving to work for Tottenham Hotspur, Bournemouth and Norwich City in Academy roles. He was appointed as first team coach at Swindon Town in November 2015 under Martin Ling, but left in May 2017 and joined Orient a month later as assistant manager.
He led the Club on its return to the Football League for the 2018/19 season but stepped back to his assistant’s role only to move back into the Head Coach role again in January 2020.
The Club expects to make an imminent announcement regarding a successor.