The USS Olympia (SSN-717), a Los Angeles-class submarine with some 120 sailors, arrived in the southern port city of Jinhae last Friday for the three-day drill.
The submarine joined South Korean naval vessels in an exercise focused on detecting enemy submarines and surface vessels in waters, near the Korean Peninsula.
"The purpose of the exercise is to increase interoperability, strengthen cooperation, and to enhance the readiness of our navies", said US Navy spokesman Arlo Abrahamson.
"These exercises are routine and regularly scheduled," he added.
Considering the all joint US-South Korean military drills as provocative rehearsals for invasion, the North Korea has repeatedly demanded they be scrapped.
Large-scale, annual military exercises -- knows as Key Resolve and Foal Eagle -- begin in early March and look set to trigger a sharp rise in military tensions on the divided peninsula.
The two Korea's have remained technically at war since, the 1950-53 Korean War concluded with a ceasefire rather than a peace treaty.
North Korea last month offered to suspend any future nuclear test, if the United States cancelled the drills this year -- a proposal rejected by both Washington and Seoul. It is not unusual for a US nuclear-powered submarine to take part.
The USS Colombia was involved in last year's Foal Eagle exercise. The 7,000-ton submarine Olympia, equipped with Tomahawk land attack missiles but without any nuclear missiles, was forward deployed from Pearl Harbor at the invitation of the South Korean Navy, Yonhap news agency said.
The United States has close to 30,000 troops permanently stationed in South Korea, and would assume command control of combined forces in the event of a conflict with the North.