The flight, which was disclosed shortly before North Korea's foreign minister was due to address the United Nations, was the farthest north of the demilitarized zone separating North and South Korea that any US fighter jet or bomber has flown in the 21st century, the Pentagon said.
He said such a test could pose a danger to shipping and aircraft, even if the North declared a "keep out" zone, and would pose a risk to people if something went wrong.
"We are prepared to use the full range of military capabilities to defend the USA homeland and our allies".
The flight follows a week of heightened rhetoric from Washington and Pyongyang, with Trump and Kim Jong Un trading insults.
North Korean leader Kim Jong-Un (L) and US President Donald Trump (R).
Moon was due to meet later Thursday with Trump and Japanese Prime Minister Shinzo Abe - their second three-way summit in two months - to show a common front in the pressure campaign against North Korea.
A small natural disaster near North Korea's nuclear test site on Saturday was probably not manmade, the nuclear proliferation watchdog and a South Korean official said, easing fears Pyongyang had exploded another nuclear bomb just weeks after its last one.
The quake was detected in an area around Kilju, in north-east North Korea.
"In this case we saw none".
September 23: The 3.4 magnitude natural disaster that hit North Korea on Saturday is said to have been caused by a fresh nuclear test.
North Korea's weakest nuclear test, the first one conducted in 2006, generated a magnitude 4.3 quake.
Vipin Narang, a nuclear expert at the Massachusetts Institute of Technology, said such a test would be worse than testing a longer range for an intercontinental ballistic missile, which is another scenario the North may be considering. "The quake is small enough to suspect that it could have been caused by a tunnel collapse, and satellite data shows there have been many landslides in the area since the nuclear test".
The United States Geological Survey was neutral in its assessment on the cause of the tremor, which it recorded as a 3.5 magnitude quake, saying in a statement that it could not "conclusively confirm at this time the nature (natural or human-made) of the event".
Tensions have continued to rise around the Korean Peninsula since Pyongyang carried out its sixth nuclear test, prompting a new round of United Nations sanctions.
The North accuses the United States, which has 28,500 troops in South Korea, of planning to invade and regularly threatens to destroy it and its Asian allies.
On Thursday Trump announced new USA sanctions that he said allow targeting of companies and institutions that finance and facilitate trade with North Korea.
Saturday's seismic activity came on the same day China announced it would limit trade with the North, reducing its fuel exports to its neighbor and banning all textile imports.