North Korea is known to be developing both nuclear weapons - it has conducted five nuclear tests - and the missiles capable of delivering those weapons to their target. Both are in defiance of UN sanctions.
South Korea said the latest test was conducted in Pukchang, in the west of the country. A missile exploded soon after take-off from Pukchang last month.
Earlier on Sunday, the North's state-run media had said it would continue to launch more "weapons capable of striking" the US.
In early May, the US said a missile defence system it had installed in South Korea was now operational.
The Thaad system can intercept North Korean missiles, although full operational capability is still some months away. North Korea and its ally China have condemned the installation of the system.
However, there is no sign that Thaad was used against the missile tested on Sunday.
Newly-installed South Korean President Moon Jae-in, who is seeking deeper engagement with the North, has convened an urgent meeting of his national security council in response.
Kim defies the pressure: Steve Evans, BBC News, Seoul
This would be the 10th detected missile launch by North Korea this year - outside experts agree that it's making progress in its stated aim of having the ability to strike the mainland US with nuclear weapons.
Though it's not there yet, the latest tests have been of missiles capable of reaching American bases in the Western Pacific, albeit with some failures.
There is intense pressure on Kim Jong-un from the US, which is seeking the help of China. Repeated and more frequent testing of missiles, despite prohibition by the United Nations, indicates the North Korean leader feels able to defy that pressure.