Stark, who took up the role of chief executive at the independent Climate Change Committee in 2018, has been critical of Prime Minister Rishi Sunak's environmental policies, saying they contradict Britain's commitment to reaching net zero carbon emissions by 2050.
"It's been a privilege to lead the Climate Change Committee team over such an important period," he said in a statement that did not specify the reasons for his departure.
In September, Stark described the UK's goal of achieving its legally binding emissions targets as "wishful thinking".
This followed Sunak's decisions to push back or slash several measures, including postponing a plan to bar the sale of petrol and diesel cars by five years.
Environmentalists and net zero proponents, including within Sunak's own party, heavily criticised the moves.
Stark's resignation comes after Conservative MP and former energy minister Chris Skidmore announced his departure last week over opposition to the development of oil and gas fields in the North Sea.
In 2019, the UK became the world's first major economy to adopt the goal of lowering fossil fuel emissions to a level of net zero by 2050.
During Stark's tenure, the CCC recommended making all new cars and vans electric by 2035 and quadrupling low-carbon electricity production in order to meet the target.
Stark's last day will be April 26, with economist James Richardson to take over in the interim, according to PA.
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