He served as Engineer, First Lieutenant and Communications Officer in the Nautilus when she was the flagship of Submarine Division Twelve, based at Pearl Harbor.

She also delivered 9,000 gallons of aviation fuel, 200 100-pound bombs and a number of US Army Air Corps pilots to Tulagi.

"For conspicuous gallantry and intrepidity in action in the performance of his duties in the USS Amberjack during a war patrol of that vessel..." he was awarded the Silver Star.

The citation further states: "As Assistant Approach Officer, his outstanding skill, excellent judgement and thorough knowledge of attack problems assisted his Commanding Officer considerably in conducting a series of successful torpedo attacks, which resulted in the sinking and damaging of enemy ships totalling more than 43,000-tons.

In addition, he was of great assistance in conducting a successful reconnaissance of four enemy positions and completing a vital special mission, contributing immensely to the success of his vessel in evading extremely severe enemy countermeasures..." Clarey made one additional patrol to the South Pacific as a prospective commanding officer (PCO) in the submarine Peto (SS-265).

Clarey was awarded the Navy Cross with the following citation: For extraordinary heroism as Commanding Officer of the USS Pintado, during the first war patrol of that vessel in enemy Japanese-controlled waters, from May 16 to July 1, 1944.

Maneuvering his ship through powerful escort screens, Lieutenant Commander Clarey launched repeated aggressive attacks to sink three Japanese freighters and damage a large freighter despite severe hostile countermeasures...He was awarded a second Navy Cross, denoted by a Gold Star affixed to the suspension and service ribbon of his original medal, "For extraordinary heroism during Pintado's second war patrol in enemy-infested waters from July 24, 1944 to September 14, 1944".

He was awarded a third Navy Cross, denoted by a second Gold Star affixed to the suspension and service ribbon of his original medal, for Pintado's third war patrol, in enemy-controlled waters of the South China Sea, between October 9, 1944, and January 1, 1945.

Clarey was selected for promotion to Rear Admiral in July 1958 and in August 1958 was assigned as Director for Military Personnel Policy in the Office of the Secretary of Defense (OSD).

In July 1962, Rear Admiral Clarey again reported to Pearl Harbor as Commander Submarine Force, U.S. Pacific Fleet (COMSUBPACFLT).

Returning to the Office of the Chief of Naval Operations (OPNAV) in June 1967, Vice Admiral Clarey assumed the duties of Director, Navy Program Planning and Budgeting.

In December 1970, he returned to Pearl Harbor as Commander in Chief, U.S. Pacific Fleet (CINCPACFLT) in what was to be his terminal assignment.

A long-time supporter of the Boy Scouts of America, Admiral Clarey was presented the Silver Beaver Award in 1976.