Simon Heale, along with his colleague Sally O’Brien, began sitting in the region in May 2019.
Their roles were introduced to relieve some of the judicial load from under-pressure District Court judges.
A Ministry of Justice spokeswoman confirmed to the Otago Daily Times that Mr Heale would leave the role at the end of the year.
"The process to seek a replacement will begin shortly," she said.
Community magistrates have the jurisdiction to sentence anyone on offences punishable by up to three months' imprisonment (although they cannot impose imprisonment) and may preside over trials for offences carrying a maximum penalty of a fine up to $40,000.
In practice it means the majority of matters they deal with are related to driving.
Dunedin and Invercargill District Court have a magistrate visiting about three times a month and there are less frequent sittings in Queenstown.
Across the country there are 14 community magistrates, based in Auckland, Waikato, Wellington and the South Island.
