The last flight by United States bombers was 17 days earlier when four US F-35B stealth fighter jets and two B-1Bs flew over the peninsula.
The South Korean Unification Ministry could not confirm that the complex has been reopened, but did say that recent bus movements and illuminated street lamps in the site have been observed.
When it first opened in 2004, the Kaesong complex, located about 54 kilometers northwest of Seoul, was meant to promote inter-Korean development and give North Korean workers a taste of life in the south, including snack foods like the cakes known as Choco Pies and toiletries that were resold as luxury items in the North.
South Korean and US government officials have been raising their guard against more North Korean provocations with the approach of the 72nd anniversary of the founding of North Korea's ruling party, which fell on Tuesday.
Trump was briefed by Secretary of Defense James Mattis and Chairman of the Joint Chiefs of Staff General Joseph Dunford at a national security team meeting, the statement said.
The B-1Bs also conducted exercises with Japan's Air Force in what the U.S. statement called a "sequenced bilateral mission".
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Donald Trump may be planning to visit the demilitarised zone (DMZ) separating North and South Korea, it has been claimed.
South Korea's 10-year bond yields have gone from a low of 2.105 percent in June to a two-year high of 2.435 percent on September 28 amid wider geopolitical concerns about the Korean peninsula.
The United Nations Security Council, which has imposed a series of ever tighter sanctions on North Korea, has banned four ships from ports globally for carrying coal from North Korea, including one vessel that also had ammunition.
Mr Trump is expected to send a "significant message" to North Korea either verbally or "kinetically" during the trip, Yonhap said, without elaborating on what that may mean.
"We reiterated our support for our collective strategy of maximum diplomatic and economic pressure on North Korea so it will be compelled to return to the negotiating table".
South Korean warships including the nation's first Aegis destroyer, Sejongdaewang (L), in this file photo. Previously, North Korean hackers were suspected of having a hand in launching cyberattacks against South Korea's air force and military.