The trilateral exercise on Sunday will be the first of its kind conducted near the Korean peninsula, an unnamed military source told Yonhap news agency.
An official at Seoul’s defense ministry declined to confirm the reports, but said the three countries were expanding joint exercises “to counter missile and nuclear threats from North Korea”, AFP reported.
Pyongyang views all such exercises as rehearsals for invasion and has repeatedly warned it would take “overwhelming” action in response.
“The South Korea-US-Japan joint aerial exercise will consist of a formation flight with the US strategic bomber B-52 escorted by fighter jets of the three countries,” a source told Yonhap.
The bomber landed at a South Korean airbase on Tuesday after first making a flyover at the country's largest defense exhibition.
Its arrival followed a port visit last week by the nuclear-powered aircraft carrier USS Ronald Reagan, which provoked an angry response from Pyongyang.
B-52s, which fly at subsonic speeds, can travel more than 8,800 miles without refueling at an altitude reaching 50,000 feet.
Pyongyang baulks at Washington’s deployment of such long-range military assets and in 2017 threatened to “shoot down” US strategic bombers even outside North Korean airspace.
Sunday's exercise comes as Seoul, Washington, and Tokyo beef up trilateral defense cooperation.
In August, the leaders of the three countries met for a summit at Camp David, agreeing to a multi-year plan of regular joint exercises and to share real-time data on North Korea.
Last week, the three countries staged a joint maritime drill in waters south of the Korean peninsula for the first time in seven years.
The two-day drill simulated intercepting North Korean smuggling vessels, Seoul's navy said.