South Korea's military said the missile flew about 450 kilometres toward the North's eastern waters.
Hours later, it said the North launched another projectile off its eastern coast but gave no further details as to what type of weapon it was.
The South Korean military said it had boosted its surveillance posture and was closely exchanging information on the launch with the United States and Japan.
South Korea's presidential office urged North Korea to immediately halt ballistic missile launches that are banned by UN Security Council resolutions. It said South Korea held an emergency national security council meeting to discuss the launch.
Japan's Defense Ministry said it noted a suspected North Korean missile earlier Sunday but that the missile did not land in its territorial waters. It did not elaborate on where it landed.
The launches came as North Korea engaged in a run of weapons tests even after US President Donald Trump scaled back a military exercise with South Korea last month in an apparent effort to revive diplomacy with leader Kim Jong Un.
Kim's sister and senior official, Kim Yo Jong, shrugged off Trump's overture, saying that shortening the drill wouldn't change its "provocative, aggressive nature."
North Korea's military later launched about 10 short-range ballistic missiles toward the sea, apparently following through with a previous threat to respond to the US-South Korean drill.
On Friday, Kim's sister slammed another recent US-led multilateral maritime exercise in the region as a "frantic military move" by the Americans meant to prolong their hegemony in the Asia-Pacific area.
The "Pacific Vanguard" exercise brought together the US, South Korea, Japan, Australia, New Zealand and Canada.
Earlier this month, North Korea conducted what it called a joint live-fire drill involving missiles, artillery and drones, a day after the United States, South Korea and Japan wrapped their five-day trilateral military drill that North Korea described as a provocation.
North Korea said its drill included firing different types of weapons simultaneously, likely aiming at developing the ability to overwhelm South Korean and US air defences.
Kim Jong Un has been focusing on expanding his nuclear arsenal after his earlier high-stakes diplomacy with Trump collapsed in 2019.
When Trump ordered the Pentagon to "substantially reduce" the annual Ulchi Freedom Shield exercise with South Korea, he cited what he called a good relationship with Kim, who has called such drills invasion rehearsals.
Emboldened by his advancing nuclear arsenal and deepening ties with Russia and China, experts say Kim likely thinks he now has greater leverage in possible fresh diplomacy with Trump.
Earlier this year, Kim said he could return to talks if the US dropped its "hostile policy" against his country and respected what he called the North's status as a nuclear state.
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