The history of NS Pearl Harbor does not begin and end with the attack in 1941. Navy interest in Hawaii goes back to the late 19th Century, when Hawaii provided the single best, most dominating strategic pivot point of the Pacific Ocean. The Navy began improving its facilities in Hawaii in 1899, leading to a coal depot, NS Honolulu (soon changed to NS Hawaii). The station had limited docking and watering facilities, and an improved station, Naval Station Pearl Harbor, was opened in 1908 to provide better support and resupply.

NS Pearl Harbor was the center of far reaching and general improvements in a long term program from 1900 to 1919. By the end of this period the station added a Marine barracks and other onshore housing and warehousing, a coaling station, machine shop, smithy, foundry, shipyard, naval magazine, and naval hospital. An airfield was established at nearby Ford Island.

Through the 1920s and 1930s Pearl Harbor was one of the bases at the center of a series of Fleet Problems, essentially wargame maneuvers. Among these exercises were scenarios similar to later World War Two battles, including the attack on Pearl Harbor and Midway. As the 1930s went on, tensions between the USA and the Empire of Japan ramped up, over Japan's military actions in China, East Asia, and the West Pacific. Japan eventually determined that a war plan against the US was required in case diplomacy broke down (the US did the same), and a plan was made to knock the US military out of war in a surprise attack. This plan resulted in the Attack on Pearl Harbor.

On Sunday 7 December 1941 an attack force of 6 aircraft carriers, 408-408 airplanes, 2 battleships, 3 cruisers, 9 destroyers, 8 tankers, 23 submarines and 4 midget submarines attacked in two waves. A detailed account of this attack can easily be found elsewhere. The attack was launched before any declaration of war, with the goal of destroying American morale, crippling the Pacific Fleet of the US Navy, and reducing American forces ahead of oncoming shipbuilding. Four battleships were sunk, four damaged, plus one battleship hull target ship sunk; several other ships were sunk, and many damaged; 188 aircraft were destroyed, 159 damaged, and 2,404 American killed (including 60 civilians). Very few of the shore facilities were seriously damaged, a strategic blunder.

The attack was a tactical victory and operational success, but a massive strategic failure. The US was enraged; the Fleet was wounded but not crippled - no carriers were present, having been deployed on operations; and the US's oncoming wave of shipbuilding grew larger. Within six months Pearl Harbor was a launching station in the Battle of Midway, which mauled the Japanese fleet, and had pulled a feat of shipyard repair in repairing USS Yorktown to battle ready condition in only 72 hours, after being badly damaged in the Battle of the Coral Sea. In four years Japan was defeated, largely because of the basing and transhipping efforts at Pearl Harbor.

Following the war NS Pearl Harbor continued to be the most vital strategic link for the USA in the Pacific Ocean through the Cold War, but as such a vital link, and the Navy having learned the lesson, most of the activity through Pearl has been logistical support of many operations in the Korean War and the Vietnam War, as well as many operations in the long Cold War.

In 2010 Pearl Harbor was joined with Hickam Air Force Base to form Joint Base Pearl Harbor-Hickam, as part of base realignment and closure budget cuts.