The Manchester United and England legend joined the Rams back in January 2020 as a player-coach, but transitioned into temporary charge following Phillip Cocu's departure.
Rooney officially hung up his boots in January 2021 and became Derby's permanent boss. He quickly earned praise for the way he handled a challenging situation at the club.
County were put into administration at the start of the 2021/22 campaign, and were relegated from the Championship despite putting on a valiant display in the face of a 21-point deduction.
Rooney informed Derby on Friday he wanted to be relieved of his duties. In a statement, he said: "Over the course of the summer I have been closely following developments regarding the ownership of Derby County," England and United's all-time top scorer said.
"Today I met with the administrators to inform them of my decision that it was time for me to leave the club. In fairness to them, they tried tremendously hard to change my decision but my mind was made up.
"My time at the club has been a rollercoaster of emotions, both highs and lows, but I have to say that I have enjoyed the challenge.
"Personally, I feel the club now needs to be led by someone with fresh energy and not affected by the events that have happened over the last 18 months.
"I will remember my time at Derby with great pride and affection and would like to thank all my staff, players and of course the fans for their incredible support.
"I will never forget you and hope to see you all again in the near future and in happier times.
"Finally, I am aware that the club still have interested parties who wish to take over the running of the club.
"To them I say this, Derby County is a great club with a great history and great fans. I wish you all the best and much success for the future."
Derby are preparing for their first season in the third tier since 1986, and those preparations will now continue without Rooney.
The club, who are still in administration and are yet to find a new buyer, take on Bradford City in their opening game of the new season on July 9.