The Southern District Health Board says chief executive Brian Rousseau made his own decision to resign and was not pushed.
Mr Rousseau's resignation and departure in December this year was announced on Tuesday.
He headed the Otago District Health Board for seven years before leading the merger with the neighbouring Southland DHB in May last year to create the Southern DHB.
The new DHB has battled a $15 million deficit, which it looks set to halve, and faced problems with services including access to diagnostic tests and elective surgery.
This prompted the National Health Board to assess systems at Dunedin Hospital. The board is also helping to sort out a row over services in Queenstown.
Mr Rousseau could not be contacted on Wednesday, but Southern DHB acting chair Paul Menzies says Mr Rousseau decided during a period of leave recently that it was time to move on.
Mr Menzies says the DHB is in good heart to withstand the challenges it faces.
The industrial adviser for the Nurses Organisation, Glenda Alexander, says Mr Rousseau gave the former Otago DHB, in particular, much-needed stability and he will be missed.
A search for a new chief executive will begin immediately.