The move, expected to occur next month, comes as the VA has ramped up its search for an under secretary for health -- a position that has been vacant since January 2017, when Dr. David Shulkin was promoted from the position to become secretary.
Stone became executive in charge of the department -- essentially fulfilling the duties of the under secretary position but without the title -- in 2018.
VA Secretary Denis McDonough announced the pending departure Thursday.
"I respect his decision to leave, especially given the reason he told me he would do so: to ensure the incoming under secretary, whom I strongly believe needs to be confirmed by the U.S. Senate, has the opportunity to fully assume leadership of the Veterans Health Administration," McDonough said in a statement.
Stone was named acting secretary of the VHA on Jan. 20, the day President Joe Biden was inaugurated. As part of former President Donald Trump's initiatives to decrease the size of the federal bureaucracy, under secretary and deputy positions often went unfilled while the duties of those jobs were performed by federal employees.
The VA established a commission in March to identify candidates for the position of under secretary. Stone's departure may indicate an announcement is imminent.
As acting under secretary, Stone was responsible for an $87.5 billion health care system that serves more than 9 million veterans. He will be remembered for steering the department and patients through the COVID-19 pandemic, related research and vaccinations, McDonough said.
"We owe Dr. Stone an immense debt of gratitude for his leadership, especially during the pandemic. When COVID-19 first began to spread, Dr. Stone was among the first people veterans and their families heard from, delivering a simple and urgent message: 'We are going to be here [for you] just like we have been for the last 100 years,'" McDonough said. "Under Dr. Stone's leadership, VHA's excellent employees have done exactly that -- vaccinating millions, saving lives and risking everything to serve those who served our country."
A dermatologist by training, Stone joined the VA in 2018 from Booz Allen Hamilton, where he worked in military health. He had previously served as principal deputy under secretary of health at the VHA. As a member of the Army Reserve, he served as deputy surgeon general and deputy commanding general of support for Army Medical Command.
His military awards include the Legion of Merit, Bronze Star and Combat Action Badge.
"As much as I hate to see Dr. Stone go, I am grateful to him for staying through mid-July," McDonough said. "I'm proud to call Dr. Stone a friend, and I thank him for his decades of service. Our nation is safer, and our veterans are healthier because of his work."
-- Patricia Kime can be reached at Patricia.Kime@Monster.com. Follow her on Twitter @patriciakime.