Magruder entered the United States Naval Academy on 3 September 1885, graduating in June with the Class of 1889, and was commissioned ensign on 1 July 1891.

[1] Following graduation from the Naval Academy, he was assigned to the protected cruiser USS Charleston, and while with that ship was commended for courage and presented a gold watch on 11 May 1890 for saving the life of a woman from drowning.

From 1891 to 1893, he served aboard the schoolship USS Monongahela, built as a barkentine–rigged screw sloop-of-war, at the Naval Training Station, Newport, Rhode Island, then on USS Kearsarge in 1894, and was aboard when she was wrecked on a reef off of Roncador Cay in the Caribbean Sea on 2 February of that year.

[1] Magruder then served aboard USS Miantonomoh, an Amphitrite-class monitor, later in 1894, and was then ordered to shore duty in the Navy Department.

"By Act of Congress he was advanced five numbers in grade for 'Eminent and conspicuous conduct in battle' for cutting cables under fire at Cienfuegos, Cuba.

In August 1917, he was ordered to command Squadron 4, Patrol Force and took six sub-chasers, 12 mine sweepers, a tender and the USS Wakiva (his flagship) to the west coast of France.

On 26 January 1918, his flagship USS Guinevere ran aground and was wrecked off the French coast with no loss of life.

Magruder commanded the naval guard for the United States Army world flight in 1924, from Scotland to Boston, via Iceland, Greenland, Labrador, Newfoundland and Nova Scotia.

On 24 September 1927, the Saturday Evening Post published an article by Admiral Magruder entitled "The Navy and Economy".

In it "he contended that the Navy was top-heavy with officers, hamstrung by red tape and burdened with idle ships and shipyards, and as a result was wasting 35 [cents] out of every dollar it spent.

[1] He received a telegram from Secretary of the Navy Curtis D. Wilbur which read: Magruder stated that the order came as a "distinct shock" to him.

Although he had been aware that his magazine article had not met with the approval of some naval officials, he stated that he hoped the matter would be straightened out.

Rear Admiral Richard H. Leigh, chief of the Bureau of Navigation, made public correspondence between the department and Magruder following his critical magazine article.

Wilbur's visit to the Executive Mansion was for the express purpose of delivering Magruder's letter seeking the interview.

[8] During the admiral's period of inactivity, he penned a volume, The United States Navy, giving a "snapshot" of the naval service as it was between the two world wars.