While Seoul works to identify the specific type of missile, the JCS said it exploded immediately after it was fired from South Hamgyong Province at about 6.20 a.m local time (2120GMT).
"The North attempted to launch a missile, but we presume that the launch ended in failure," a JCS official was quoted by local news agency Yonhap.
Pyongyang has repeatedly drawn international condemnation for ignoring United Nations resolutions that bar its development of nuclear weapons. The launch Sunday came as speculation mounts about reported U.S. plans for a pre-emptive strike.
Washington has dispatched a nuclear-powered aircraft carrier group to the region and U.S. Vice President Mike Pence is scheduled to make his first official visit to South Korea later Sunday.
North Korea has warned it will soon test an intercontinental ballistic missile capable of striking the U.S. mainland, as the reclusive state paraded three ICBMs during a massive military parade Saturday to celebrate the 105th birthday of late national founder Kim Il-sung.