The phase one of his physical came nine months after his last annual exam that was conducted in one visit.
His last visit to the Army medical center was not previously announced by the White House though his two previous trips were noted ahead of time on his daily schedule.
Trump, 73, departed the White House at 2:15 p.m. in a motorcade and arrived at Walter Reed at 2:47 p.m., according to a White House pool report. In past medical exams, he took the Marine One helicopter.
"Anticipating a very busy 2020, the president is taking advantage of a free weekend here in Washington, D.C., to begin portions of his routine annual physical exam at Walter Reed," White House press secretary Stephanie Grisham said in a statement.
Trump is seeking his second term as president next year.
The results of the "quick exam and labs" were not announced.
"The President remains healthy and energetic without complaints, as demonstrated by his repeated vigorous rally performances in front of thousands of Americans several times a week," Grisham said in a followup statement 2 1/2 hours after he arrived at Walter Reed.
"The president also stopped by to say hello to the medical staff of Walter Reed, to share his thanks for all the outstanding care they provide to our Wounded Warriors, and wish them an early happy Thanksgiving."
It was the president's ninth visit to Walter Reed.
"Before leaving he met with the family of a special forces soldier injured in Afghanistan," Grisham said.
Trump posted on Twitter after midnight: "Visited a great family of a young man under major surgery at the amazing Walter Reed Medical Center. Those are truly some of the best doctors anywhere in the world. Also began phase one of my yearly physical. Everything very good (great!). Will complete next year."
On Feb. 9, Trump underwent a physical that lasted four hours. He was deemed to be in "very good health overall" by the president's physician, Dr. Sean Conley.
He weighed 243 pounds, which is an increase of four pounds from his previous exam, and his blood pressure was 118/80.
"While the reports and recommendations are being finalized, I am happy to announce the president of the United States is in very good health and I anticipate he will remain so for the duration of his presidency and beyond," Conley said in a memorandum released by the White House one day after the exam.
Trump's exam in 2018 was performed by Dr. Ronny Jackson, who nominated him to be the next secretary for veteran affairs but withdrew his name from consideration for the post amid accusations of ethical misconduct, including that he recklessly prescribed drugs and wrecked a government vehicle.