Chief Minister Natasha Fyles met NT Administrator Vicki O'Halloran on Thursday to ask for the writs to be issued for a poll in the Fannie Bay electorate on August 20.
Mr Gunner has held the seat since 2008 and was returned at the 2020 election with a margin of 9.6 per cent.
But with that translating to just 833 votes, Ms Fyles urged locals to continue to support Labor.
"All elections offer a choice for Territorians and the choice in this by-election is clear," she said.
"A choice between a strong, stable Territory Labor government or a CLP opposition who have no plans, no solutions and no ideas."
Mr Gunner, who was the first Territory-born Top End leader, took control of the then-opposition in 2015.
He led Labor to a landslide victory in 2016 before his government was returned easily two years ago, partly on the back of its handling of the COVID-19 pandemic.
The 46-year-old has been on the back bench since May when he resigned from the top job.
On Wednesday evening he announced he was quitting parliament in a speech to the NT Legislative Assembly.
"In May I stepped down as chief minister. Tonight I resigned as the Member for Fannie Bay. The reasons are the same: what is best for the people I serve and what is best for my family," Mr Gunner wrote on Facebook.
"This job, being a member, is one that is and should be all-consuming ... I don't know any other way than going full-on."
He said "my method was not the healthiest approach", with a heart attack in 2020 providing something of a wake-up call.
"I will miss this place, my fellow members, my friends. (Natasha Fyles) and the team are doing an amazing job. The Territory is in safe hands.
"I will work again. I'm not in a position to retire for life. I have no plans yet and I can't see myself working again until late this year at the earliest but my priorities are clear.
"My family come first, supporting my wife, raising my boys."
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