The missile fell into the Pacific Ocean after flying over the island of Hokkaido.
South Korea’s military said the ballistic was fired from the Sunan district of Pyongyang.
It comes two weeks after North Korea fired a different missile over northern Japan, sparking panic as people were told to take cover before it broke into three pieces and fell into the waters off Japan’s Hokkaido island.
The country’s J-Alert warning signal told people to shelter in a ‘sturdy building or basement’.
Today’s missile flew significantly further than the one in August, with this one travelling around 2,299 miles.
Following the previous launch, Foreign Secretary Boris Johnson said he was ‘outraged’ by the ‘reckless provocation’.
Japan’s Chief Cabinet Secretary Yoshihide Suga said it was an ‘unprecedented, serious and grave threat to our nation,’ adding the government had protested the move in the strongest terms.
The Japanese military did not attempt to shoot down the missile.