Puffer was transported down the Mississippi to New Orleans on a special floating drydock, having periscope shears re-installed en route.

Puffer′s first war patrol, to intercept Japanese commerce in the Makassar Strait–Celebes Sea area, 7 September to 17 October, resulted in several damaged ships but no sinkings.

She acted as life guard for the first Allied carrier strike on Soerabaia, sank 3,181-ton freighter Shinryu Maru 18 May, then on 5 June, attacked three tankers, sinking 2,166-ton Ashizuri and 2,500-ton Takasaki.

Refitted at Midway she departed 20 May en route to the South China and Java Seas to conduct her eighth war patrol.

Completing her ninth patrol with the cessation of hostilities in mid-August 1945, Puffer headed for Subic Bay, thence to the United States, reaching San Francisco 15 October.

Employed in that status, at Seattle, until relieved by USS Bowfin (SS-287) 10 June 1960, Puffer was placed out of service and sold for scrapping to the Zidell Corporation, Portland, Oregon, on 4 November 1960.

Puffer earned 9 battle stars for World War II service in the Pacific Theater, with a total tonnage of 36,392 tons (eight ships).