Ged Fitzgerald was arrested along with Lancashire County Council leader Geoff Driver and two others as part of a probe into witness intimidation.
The four have been on police bail ever since.
Mr Fitzgerald was being investigated over his time spent as Chief Executive of Lancashire County Council, but has since moved to Liverpool.
He was suspended from his role on Liverpool council after the arrests in May last year, but announced yesterday that he would be resigning.
Liverpool Mayor Joe Anderson said he had accepted his resignation.
In a statement, Mr Anderson said: "Ged Fitzgerald has resigned from his post as CEO of Liverpool City Council with immediate effect.
"I can confirm that he wrote to me this morning and tendered his resignation, which the council has accepted."
Mr Fitzgerald and Councillor Driver were arrested along with Phil Halsall and David McElhinney on suspicion of conspiracy to pervert the course of justice and witness intimidation.
The arrests were in connection with the long-running probe into the One Connect contracts.