The “unidentified ballistic missile” was launched at around 2057 GMT Monday from Sunan, near Pyongyang, the South’s Joint Chiefs of Staff said in a statement, saying it travelled east “and over Japan”.
“South Korea and the US are jointly analysing for details,” it added.
Tokyo also said it overflew its territory, with Prime Minister Shinzo Abe saying the government would take “full steps” to ensure the safety of the Japanese people.
The country’s chief government spokesman, Yoshihide Suga, said the missile posed a “serious, grave security threat” to Japan.
The firing comes days after Pyongyang launched three short-range missiles in what was seen as a minimal provocation after the start of the Ulchi Freedom Guardian South Korean-US joint military exercises.
But Tuesday’s flight path represents a significant escalation by Pyongyang, which earlier this month threatened to fire a salvo of missiles towards the US territory of Guam.
Any such flights would have to pass over Japan.
When Pyongyang carried out its first two successful tests of an intercontinental ballistic missile (ICBM) last month it fired them on lofted trajectories that avoided travelling over the Asian island nation.
Japan has in the past vowed to shoot down North Korean missiles or rockets that threaten to hit its territory, and deployed its Patriot missile defence system in response to the Guam threat, reports and officials said, with an Aegis destroyer also stationed in the Sea of Japan (East Sea).
In 2009, a North Korean rocket passed over Japanese territory without incident, triggering Japan’s immediate denouncement.
At the time North Korea said it was launching a telecommunications satellite, but Washington, Seoul and Tokyo believed Pyongyang was testing an ICBM.