The missile was launched at around 9.10am local time from an airfield in Panghyon, about 100 km (60 miles) northwest of the North’s capital, Pyongyang, the South Korean military said.
The rocket flew for about 40 minutes and may have landed in Japan’s Exclusive Economic Zone (EEZ), the Japanese government said.
The US President was quick to react on Twitter, asking “does this guy have anything better to do with his life?”
The launch is the last since Pyongyang fired several cruise missiles in early June.
It comes as the leaders of the United States, China, Japan and South Korea are expected to discuss efforts to rein in the North’s nuclear and missile tests the G20 summit on July 7 to 8.
Pyongyang has been working to develop a nuclear-tipped missile capable of hitting the United States.
Earlier this week, North Korea was a key topic in phone calls between President Donald Trump and the leaders of China and Japan.
Leaders of both Asian countries reaffirmed their commitment to a denuclearised Korean Peninsula.
Tuesday’s missile launch also comes ahead of July 4 Independence Day celebrations in the United States.
North Korea has previously fired missiles around this US holiday.
South Korea’s presidential Blue House said President Moon Jae-in called a national security council meeting for 2.30am GMT after being informed of the North’s missile launch.
Last week after his first summit with Moon, Trump called for a determined response to North Korea, stressing the importance of the alliance between the two countries.
Last month, North Korea carried out another test of a rocket engine, believed to be part of its programme to develop an intercontinental ballistic missile.
The US fears the test, the latest in a series of engine and missile tests this year, could be for the smallest stage of an ICBM rocket engine, an official said.
It is not known what type of rocket component was tested or whether it fit into the ICBM programme, another official told Reuters.
The 22-year-old died on Monday after suffering a severe brain injury while being held prisoner in North Korea.
The disclosure of the engine test also came a day after the US pressed China to exert more economic and diplomatic pressure on North Korea to help rein in its nuclear and missile programmes during a round of high-level talks in Washington.
Donald Trump has warned that a “major, major conflict” with North Korea is possible over its weapons programmes, although officials say tougher sanctions, not military force, are the preferred option.
The head of the US Defense Intelligence Agency told Congress last month that North Korea, if left unchecked, was on an “inevitable” path to obtaining a nuclear-armed missile capable of striking the US mainland.
Still, experts say Pyongyang could still be years away from have a reliable ICBM capability.
The continental United States is around 5,600 miles (9,000 km) from North Korea.
ICBMs have a minimum range of about 3,400 miles (5,500 km), but some are designed to travel 6,200 miles (10,000 km) or further.
Any military solution to the North Korea crisis would be “tragic on an unbelievable scale”, Trump’s defence secretary, Jim Mattis, said last month.
The US, meanwhile, is ramping up capabilities to defend against the threat from North Korea, staging its first-ever successful test to intercept an incoming ICBM-type missile in May.
But a test on June 21 of a new capability being developed by the United States and Japan to defend against shorter-range missiles failed to hit its target, the U.S. Missile Defense Agency said on Thursday.
It was the second such test of the SM-3 Block IIA interceptor, which is being developed by Raytheon. The previous intercept test, conducted in February, had been successful.