(CNBC) The president said in a statement that Jackson, a Navy rear admiral, "has seen firsthand the tremendous sacrifice our veterans make and has a deep appreciation for the debt our great country owes them."
Jackson, a longtime presidential physician, oversaw Trump's annual medical checkup, which he said "went exceptionally well." He also presided over Barack Obama's last physical in office in 2016.
Trump thanked Shulkin for his service and said Robert Wilkie will serve as acting secretary. Wilkie currently serves as undersecretary of defense for personnel and readiness at the Department of Defense.
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Shulkin has been under fire after an internal watchdog report revealed that the VA had improperly approved taxpayers footing the bill for a trip Shulkin's wife took with him to Europe last year.