The North fired the missile to the northeast from an area off its east coast at about 6:30 p.m. local time (0930 GMT), the South's office of the Joint Chiefs of Staff said.
North Korea will hold a rare congress of its ruling Workers' Party in early May for the first time in 36 years.
South Korea's Yonhap news agency said the missile flew "for a few minutes," citing a source. There were no further details.
The North first attempted a launch of the submarine-based missile last year and was seen to be in the early stages of developing such a weapons system, which could pose a new threat to its neighbors and the United States if it is perfected.
However, follow-up test launches were believed to have fallen short of the North's expectations as its state media footage appeared to have been edited to fake success, according experts who have seen the visuals.
South Korea's military has said it is on high alert over the possibility that the isolated North could conduct its fifth nuclear test "at any time" in defiance of U.N. sanctions after setting off what it said was a hydrogen device in January.
Satellite images show that North Korea may have resumed tunnel excavation at its main nuclear test site, similar to activity seen before the January test, a U.S. North Korea monitoring website reported on Wednesday.
South Korea and the United States, as well as experts, believe the North is working to develop a submarine-launched ballistic missile system and an intercontinental ballistic missile putting the mainland United States within range.