The test on Wednesday of what the North claimed was its first hydrogen bomb has sparked international alarm and raised tensions along the inter-Korean frontier, with Seoul reviving cross-border propaganda broadcasts.
Sunday's overflight saw a B52 Stratofortress, which is capable of carrying nuclear weapons, briefly roar over the Osan Air Base, some 70 kilometres (45 miles) south of the inter-Korean border, the US military and an eye-witness said.
It was escorted by a South Korean and an American jet.
The B52 conducted a low-level flight before heading back to Andersen Air Base in Guam, where it is stationed.
The mission was conducted "in response to recent provocative action by North Korea", US Forces Korea said in a statement.
The aircraft are known to have taken part in joint annual US-South Korea military exercises that have enraged Pyongyang, but their flights over South Korea are rarely publicised. The last time such a flight was made public was in 2013, after North Korea carried out its third nuclear test.
At that time, the US dispatched both a B52 and the more sophisticated B2 stealth bomber to South Korea in a show of military muscle against the North.