The launch comes after US President Donald Trump's renewed invitation for talks with Pyongyang.
South Korea's military said the unidentified missile was launched from an area in North Korea's northwest region near the Chinese border and fired towards the sea to the east.
The Japanese government also said North Korea had fired what could be a ballistic missile, which likely fell outside of Japan's exclusive economic zone.
Prime Minister Sanae Takaichi said there was no confirmed report of damage.
While visiting South Korea last week, Trump repeated his willingness to sit down with North Korean leader Kim Jong Un, raising expectations that the two could come to a last-minute agreement to meet.
No meeting took place, but Trump said he was willing to return to the region to meet Kim.
Trump met Kim at the Panmunjom truce village on the inter-Korea military border in 2019 during the US president's first term when he was visiting the region.
Kim has not responded to Trump's latest overtures but has previously said he had "fond memories" of meeting the US president and there was no reason to avoid talks if Washington stopped insisting his country give up its nuclear weapons.
On Thursday, the North's foreign ministry said the Trump administration was "antagonising" it by imposing sanctions on its officials and institutions over allegations of money laundering.
North Korea fired multiple short-range ballistic missiles, including what it said was a hypersonic missile, and sea-to-surface cruise missiles last month ahead of the visit by Trump and Chinese President Xi Jinping to South Korea during a regional summit.Â
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