Trump announced the move in a Twitter post early Saturday morning, which comes amid ethics investigations into Zinke.
"Zinke will be leaving the Administration at the end of the year after having served for a period of almost two years," Trump tweeted. "Ryan has accomplished much during his tenure and I want to thank him for his service to our Nation."
Zinke, a former Navy SEAL, later explained on Twitter why he felt it was time to leave the position.
"I love working for the President and am incredibly proud of all the good work we've accomplished together," Zinke tweeted. "However, after 30 years of public service, I cannot justify spending thousands of dollars defending myself and my family against false allegations."
Zinke entered the position in March 2017 facing criticism from environmental groups over his position against endangered species protections. He rode into the position the first day on horseback, and rescinded an Obama administration order banning lead ammunition and fish tackle on wildlife refuges.
He became "one of the most ethically dubious members of President Trump's Cabinet," after taking office, social media manager Caroline Zhang of Citizens for Responsibility and Ethics in Washington, a nonpartisan ethics watchdog, wrote in a blog.
The blog addressed 17 federal investigations into Zinke's behavior since he became secretary of the interior.
"While a few of these investigations have cleared Zinke of wrongdoing, many remain ongoing, and -- perhaps most concerning -- several were closed or were inconclusive due to a lack of cooperation with the probe or the Interior Department's failure to keep proper records," Zhang wrote.
Among the most recent scandals are a blocked casino project and a potential Hatch Act investigation after Zinke tweeted a photo on his government account that including Trump's political slogan.