David Hinchliff, who will leave next March, said he had been planning his retirement for some time and that “the time is now right to hand the service over.”
The YEP revealed in February that he was under investigation by an official watchdog over remarks made at an inquest of a West Yorkshire police officer who took his own life.
A month earlier, it emerged that Mr Hinchliff had been banned from driving for six months after racking up 12 penalty points for speeding in three years.
He has been overseeing inquests in Leeds and Wakefield for 24 years and first became a coroner in 1987.
Mr Hinchliff said: “I have had a long, interesting and satisfying career, which at times has been challenging and demanding.
“No two days are the same but it has been a privilege to be able to help the families of those who have died to have an understanding of the circumstances of the death. In the majority of cases it can help people get some sort of closure.
“The job has changed considerably since I became a Coroner, and families, rightly, no longer accept without reservation what the medical profession tells them.
“I will be sad to leave the service but I believe the time is now right to hand the service over.”
Wakefield council said in a statement that Mr Hinchliff had been planning his retirement for some time and had “made a number of changes in recent years to allow this to happen with minimal disruption to the service and public”.
Michael Clements, Wakefield Council’s Assistant Chief Executive for Resources and Governance, said: “Mr Hinchliff has provided an invaluable service for thousands of families across the region, supporting them to gain answers when they need them the most.
“During his career he has successfully overseen the implementation of the Coroners and Justice Act in 2013 and the move to one court base in Wakefield.
“We will be working closely with Leeds City Council and West Yorkshire Police to ensure that another successful Senior Coroner is appointed to carry on the important service that Mr Hinchliff has provided across Leeds and the Wakefield district.”
In February, it emerged that Wakefield Coroner’s Court had been forced to draft in extra workers from other parts of the region after staff shortages left a backlog of more than 100 cases waiting to be looked into.
West Yorkshire Police issued an apology after admitting that “significant” staff shortages had impacted services to the public.