After the outbreak of the Civil War, he was reassigned to the brig USS Perry on Atlantic coast blockade duty from May to November 1861.

In March 1862, his vessel towed the frigate USS St. Lawrence into action during the first day of the Battle of Hampton Roads.

[2][3] From September 1862 to June 1863, Miller served as executive officer of the monitor USS Passaic in the South Atlantic Blockading Squadron.

He was commended by his commanding officer for his actions during both the first and second naval attacks on Fort Fisher, North Carolina in December 1864 and January 1865.

From October 1867 to January 1870, he was executive officer of the sidewheel steam frigate USS Powhatan in both the Pacific and North Atlantic Squadrons.

[3][5] From April 1870 to November 1872, Miller served as chief of staff of the Pacific Squadron and commanding officer of the screw sloop-of-war USS Ossipee.

He performed a line of deep sea soundings between Honolulu and Brisbane and made a reconnaissance visit to Samoa.

From May to August 1882 and from September 1883 to October 1884, Miller was chief of staff of the North Atlantic Squadron and commander of the screw frigate USS Tennessee.

[3][6] From May 1891 to June 1892, Miller served as commanding officer of the protected cruiser USS Chicago, flagship of Rear Adm. John G. Walker in the Squadron of Evolution.

Promoted to rear admiral on 21 March 1897, he was detailed in May 1897 to represent the U.S. Navy at Queen Victoria's Diamond Jubilee with his flag on the armored cruiser USS Brooklyn.

[2][11] In July 1898, Miller returned to Honolulu with his flag on the protected cruiser USS Philadelphia for the impending annexation of Hawaii.

In Autumn 1856, he was elected justice of the peace for Springfield Township and held that post until his retirement in Fall 1874 at the age of seventy-seven.