In a video posted on YouTube on Thursday night, Perry said that his departure would come later this year but did not give an exact date, Efe news reported.
"There is much work to be done in these upcoming weeks and I remain fully committed to accomplishing the goals that I set out to accomplish at the beginning of my tenure," the 69-year-old said in the video, adding he wanted to return to Texas, "my favourite place in the world".
At a campaign rally on Thursday night in Dallas, Trump thanked Perry, saying he "couldn't have done a better job".
The President added that said he has already picked a new Energy Secretary, but stopped short of disclosing the person's name.
Until recent weeks, Perry had one of the longest and least dramatic tenures in the Trump cabinet. But the former Texas Governor is exiting the political stage as a player in the biggest drama of Trump's presidency.
House committees were conducting an impeachment inquiry centred on Trump's efforts to pressure Ukraine into investigating matters related to US elections. The President has denied any wrongdoing.
Perry was one of the president's top intermediaries with the Ukrainian government, leading House investigators to issue him a subpoena last week for any documents related to his interactions on the matter.
Perry, in an interview with The Wall Street Journal this week, said he contacted Rudy Giuliani, the President's personal attorney, at Trump's direction in an effort to ease a path to a meeting with his Ukrainian counterpart, Volodymyr Zelensky.
He said Giuliani described to him, during their phone call, several concerns about Ukraine's alleged interference in the 2016 US election, concerns that haven't been substantiated.
Perry also defended the President several times, saying he was sympathetic to his concerns about Ukrainian corruption.
In addition, the Energy Secretary said he never heard the president, any of his appointees, Giuliani or the Ukrainian regime discuss the possibility of specifically investigating former Vice President Joe Biden, a Democratic presidential contender, and his son Hunter Biden.
Perry has had a unique role in the history of US energy secretaries, becoming a top diplomat on international energy issues in a position usually more focused on science and nuclear weapons.
Before becoming energy secretary, Perry was a two-time presidential candidate who spent 14 years as Texas Governor.
In the 2016 race, he became one of Trump's most vocal critics, but dropped out before even the first primary. Instead, he went on television as an amateur performer on "Dancing With the Stars", only to to return to government in partnership with Trump.
Several times at speeches around the US, Perry described joy about his role leading the Energy Department, a sprawling organization that oversees most US government scientists, research into new energy technologies and protection for the US nuclear weapons arsenal.
He said he loved learning about government scientists and promoting their work, in addition to fostering public-private partnerships.
( With inputs from IANS )