Yonhap news agency confirmed Wednesday's launch was towards the sea off North Korea's east coast.
South Korea's Joint Chiefs of Staff gave no further details such as how far the missile flew.
North Korea last launched ballistic missiles on May 8 when it fired multiple short-range missiles from its east coast.
North Korea rejects international ban backed by the US and South Korea among others on its ballistic missile development.
Wednesday's launch comes ahead of a visit to South Korea next week by leaders attending an Asia-Pacific economic forum, including US President Donald Trump and Chinese President Xi Jinping.
Experts earlier said North Korea could launch provocative missile tests ahead or during the APEC summit to underscore its commitment to acquiring the status of a nuclear weapons state.
Earlier this month, North Korean leader Kim Jong-un displayed a new long-range missile at a massive military parade in Pyongyang, with top Chinese, Russian and other leaders present.
The parade, which marked the 80th anniversary of the founding of the ruling Workers' Party, highlighted Kim's growing diplomatic footing and his relentless drive to build an arsenal that could target the continental United States and his rivals in Asia.
Kim's diplomatic credentials have been bolstered recently. He took centre stage with Chinese leader Xi Jinping and Russian President Vladimir Putin at a Beijing military parade last month.
Trump and South Korean President Lee Jae Myung have also repeatedly expressed hopes to meet the reclusive North Korean leader as he flaunts a provocative nuclear program.
with AP
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