Chief Constable Phil Gormley is currently the subject of five separate investigations by the Police Investigations and Review Commissioner (Pirc) amid allegations of bullying.
In a statement released today, the Scottish Police Authority said it had accepted Mr Gormley's resignation.
The chief constable, who denies any wrongdoing, has been on leave since September and had 10 months of his current contract still to run.
The SPA said it had become clear that irrespective of the outcome of the ongoing investigations, Mr Gormley would not be able to resume his operational role in Police Scotland in a "meaningful way".
Mr Gormley said: “The last eight months have been difficult for me and my family, in particular I would like to thank my wife for her love and loyalty. The events since November 2017 have led me to the conclusion that it is impossible for me to resume my duties in a meaningful way prior to the end of my contract.
"I now need to prioritise the health and wellbeing of my family on whom these events have taken a significant toll.
“The support of colleagues from across the UK with whom I have served during the last 32 years has been a source of great strength. As chief constable of Police Scotland I have had the privilege to meet and work with some exceptional people, I wish them well for the future and it is in their interests that I feel it is right to step aside.”
The SPA said the chief constable would receive a payment in respect of his salary for his 3 months’ notice period and his outstanding annual leave entitlement.
He will receive no other settlement or severance payment from the SPA.
Susan Deacon, chair of the SPA, said: “Chief Constable Gormley has made a significant contribution to policing in Scotland.
"The delivery of the 10-year strategy “Policing 2026: Serving a Changing Scotland” provides a strong basis for Police Scotland to move forward.
"I would like to thank him for this contribution and wish him well for the future. This has been a challenging period for all concerned, and in the interest of policing in Scotland we now need to move on”.