After shakedown out of Newport, Rhode Island, Harder made a 1000-mile (1600-km) submerged passage from New London, Connecticut, to Nassau, Bahamas, while snorkeling.

In March 1959 she participated in SUBICEX, during which she cruised 280 miles (450 km) beneath the ice packs off Newfoundland, further than any conventionally powered submarine had previously gone.

She continued operations in the Atlantic and Caribbean for more than a year, then departed Charleston 24 May 1961 for deployment off the western coast of Europe and in the Mediterranean Sea.

Training exercises and tests evaluating ASROC and other ASW systems kept Harder busy until she entered Charleston Naval Shipyard for overhaul in October 1962.Ready for action in April 1963, she operated along the Atlantic Coast and in the Caribbean Sea for the next 2½ years polishing her underwater warfare tactics and operating with destroyer-type ships as they worked on ASW exercises.

Harder again entered Charleston Naval Shipyard on 22 October for a thorough overhaul and modernization in which she received an 18-foot hull extension to accommodate the new PUFFS passive sonar system, a redesigned superstructure, new engines, and improved electrical and electronic equipment.