While the two destroyers were damaged beyond repair, Pennsylvania was quickly made war ready again since she only received one bomb hit and sailed to San Francisco on 20 December and arrived nine days later. Once her repairs were complete she departed 30 March 1942 and operated on the west coast before departing for Pearl Harbor on 1 August and arriving on 14 August. While in the Hawaiian Islands area she conducted exercises and returned again to Mare Island Navy Yard for another refit on 4 October 1942. While here she was equipped with, among other structural changes, a battery of eight twin 5in/38cal dual purpose mounts and equipped with quad 40mm Bofors and 20mm Oerlikon guns. When she left on 5 February 1943 she went on a post-refit shakedown cruise on the west coast and began to prepare for her role in the upcoming Aleutian operation in Alaska.

Pennsylvania arrived at Cold Bay, Alaska, on 30 April 1943 and sailed to Attu as flagship of Task Force (TF) 51 on 4 May. Since there was a dense fog covering the targets at Holtz Bay and Chicago Harbor she had to rely on her main and secondary battery radar for shore bombardment. Stationed about 9000 yards off the shore she provided support for the Army landings between 11-12 May. While departing on the latter day, a PBY Catalina flying boat spotted a torpedo wake aimed for Pennsylvania which provided ample warning for her to steam ahead allowing the torpedo to pass harmlessly astern. Two destroyers were immediately sent to hunt down the source - the Japanese submarine I-31 (eventually sunk on 13 June.) On 14 May, she again attacked targets west of Holtz Bay and she sent her OS2U Kingfisher floatplanes to operate from the seaplane tender USS Casco to make strafing runs on Japanese positions. While retiring for the day more torpedo wakes were seen passing astern again but the source was not found. With her Kingfishers reclaimed, she departed for Adak on 19 May. On the that day, an explosion occurred in the forward gasoline storage causing damage but no casualties. She sailed to Puget Sound Navy Yard, Washington, on 28 May and a similiar explosion occurred again on 2 June resulting in a death.

Returning again to Adak on 7 August 1943 she participated in the invasion of Kiska but on 16 August it was determined that the Japanese had in fact deserted well before the landings. During August and September she operated between Pearl Harbor and San Francisco and in October began preparing at Pearl Harbor for her next operation. On 10 November, she departed Pearl Harbor as the flagship of Rear Admiral Turner, Fifth Amphibious Force, as part of the Northern Attack Force (TF 52) for the assault on Makin Atoll, Gilbert Islands. On the morning of 20 November, TF 52 (four battleships, four cruisers, three escort carriers, transports and destroyers) arrived at the atoll from the southeast. Soon afterwards, Pennslyania began shelling Butaritari Island at the initial range of 14,200 yards. Within 90 minutes her main batterty had expelled 403 high capacity shells, and with temperatures of 115°F in the aft magazine seven men fainted. A great explosion occurred off her starboard bow while returning to a screening sector off Makin on the early morning of 24 November. A destroyer made sound contact with a submarine (I-175) and it was discovered that the escort carrier USS Liscome Bay (CVE 56) had been torpedoed and sunk with a tremendous loss of life. Japanese torpedo planes tried to attack the task force on the nights of 25-26 November but were unsuccessful.

Task Force 52 moved to Kwajalein during the first week of February 1944 with Pennsylvania shelling the island from as close as 2000 yards. On the night of 3 February, she provided star shell illumination for the ground troops operating in the north. With the operation complete, she sailed to Majuro Atoll for replenishment. While taking on 14in powder tanks from the ammunition ship USS Mauna Loa, one powder tank blew up on the forecastle of Pennsylvania and burning about 20 others in the process. Miraculously, there was not a catastrophic explosion and only a few men were injured. Before midnight on 11 February, another powder tank exploded while being handled into the ready service magazine of 'A' Turret, and again miraculously no catastrophic explosion but several men died later from their injuries.

On 17 February 1944, Pennsylvania sailed to Eniwetok, Marshall Islands, to support the landings the following days. Between 20-21 February she also bombarded Parry Island before leaving on 22 February, but not before being being closely missed by a Japanese 75mm shell. After this operation, she sailed to Efrate, New Hebrides, where she remained until late April before moving to Sydney, Australia on 29 April. In early June, she was in a fire support group of TF 52 and while on a quick turn maneuver to avoid a submarine contact on 10 June, she collided with the fast transport USS Talbot (APD 7). While Talbot had to return to Eniwetok due to extensive damage, Pennsylvania continued on with very minor damage. On 14 June, she provided pre-invasion bombardment at Saipan and Guam. While refueling destroyers on 22 June a Japanese Betty appeared and dropped a torpedo almost on her, but it hit the water a few yards off the starboard bow only to end up hitting the battleship USS Maryland.

Between 12-14 July, Pennsylvania bombarded Guam again and returned for ammunition at Saipan before returning to Guam on 17 July where she continued to provide support until 3 August. During the Guam campaign, she fired more ammunition than any other warship in history during a single campaign. She in fact earned one of her nicknames, "Old Falling Apart," because she expelled so much metal it would appear she was was falling apart.

Returning again to pre-invasion bombardment, Pennsylvania operated at Peleliu between 12-14 September and provided support during the landings on 15 September. And yet again at Anguar Island she performed shore bombardment. Between 1-12 Ocotber she was under repair at a floating drydock before arriving off the eastern entrance to Leyte Gulf, Philippines, on 18 October. She provided bombardment and support through 22 October, before becoming a part of the battleship lineup at Surigao Strait. The resulting battle on 24/25 October would cost the Japanese two battleships and three destroyers but Pennsylvania never fired due to "radar failure." She operated at Leyte for 37 days, all the while under aircraft attack. On 25 October, ten Japanese aircraft attempted an attack on a destroyer but Pennsylvania downed four and drove off the rest. And again on the night of 28 October, she shot down a Betty attempting a torpedo run.

In the first week of January 1945, she sailed to Lingayen Gulf for more bombarding which began on 6 January at Santiago Island. Throughout the next several days she continued shelling and provided fire support for the landings on 9 January. On 10 January, Japanese aircraft almost hit her with four bombs within a 31 minute period. After this she patrolled the Lingayen Gulf area before departing 22 February for the Marshall Islands, then to Pearl Harbor, to eventually arrive at San Francisco on 13 March. At Hunters Point she underwent an overhaul until departing early July. After a post-refit shakedown trial and a refresh cruise she returned to Pearl Harbor on 18 July.

While enroute to Saipan she assisted in the bombardment of Wake Island on 1 August. On 12 August she entered Buckner Bay, Okinawa and anchored alongside the battleship USS Tennessee. That night at 2045, a lone Japanese torpedo plane slipped into the bay and aimed its torpedo at Pennsylvania. The torpedo exploded on the starboard side near the stern killing 20 instantly and wounding 10 more and bending three of her four prop shafts. Many compartments on the third deck flooded and she settled heavily by the stern. More Japanese aircraft were detected and fired upon the next day while salvage operations were underway. The war ended only three days later and on 18 August two tugs towed her to Apra Harbor, Guam for temporary repairs. On 4 October she set sail under her own power for Puget Sound Navy Yard, not arriving until 24 October because of screw and shaft difficulties en route.

Pennsylvania received enough repairs in order to use her as a target ship in Operation Crossroads, the atomic bomb tests at Bikini Atoll. She survived both tests on 1 and 25 July 1946 with very slight damage and was later towed to Kwajalein and decommissioned on 29 August where she remained for radiological and structural studies until 10 February 1948. Rated too "hot" from the atomic tests and still taking on water from the 1945 torpedo hit, she was scutlled off Kwajalein Island two days later. She was awarded eight battle stars and the Navy Unit Commendation for her service in World War II.