The weapon was fired in the direction of the East Sea, South Korea’s joint chiefs of staff have confirmed.
Officials said the missile was launched around 10.55pm GMT (7.55am local time), from Banghyeon in the North Pyongan Province.
The North Korean army reportedly fired the missile Sunday morning.
The missile flew about 500km according to the South Korean military, with officials describing it as North Korea's "show of force" against the Trump administration's tough stance on Kim Jong-un’s regime.
South Korea's joint chiefs of staff said: "The flight distance was about 500 kilometres, and South Korea and the United States are conducting a close-up analysis on additional information."
The South Korean foreign ministry said the North's "repeated provocations" showed the Kim regime's "nature of irrationality, maniacally obsessed in its nuclear and missile development".
North Korea is believed to be increasing its weapons capabilities.
An anonymous US Pentagon official said: “We can confirm that we did detect a missile launch from North Korea.
“We are assessing and will have more information soon."
The US military reportedly tracked the missile and determined it to be of "medium or intermediate" range.
Kim's missile may soon be capable of reaching US shores, according to reports.
President Trump has been briefed on the launch, according to White House officials, and is continuing to monitor the situation.
Get Quotes on Home Insurance
In a press conference held with Japanese prime minister Shinzo Abe, Trump said the US stands behind the nation in the wake North Korea's move.
He said: "I just want everybody to understand, and fully know, that the United States of America is behind Japan, our great ally, 100 per cent.”
Trump held a press conference with Japanese prime minister Abe to discuss the matter.
A White House official added that the missile test meant Trump had to do more to pressure China, Kim's biggest ally, into reigning in North Korean aggression.
The alarming act of military aggression comes little more than a week after Donald Trump’s defence secretary warned North Korea it would face an “effective and overwhelming response” if it chose to use nuclear weapons.
US defence secretary James Mattis sent a stark warning to North Korean over its military aggression.
General James ‘Mad Dog’ Mattis reassured South Korea the US would continue its support amid increasing fears over North Korea’s nuclear capabilities.
He said: “Any attack on the United States, or our allies, will be defeated, and any use of nuclear weapons would be met with a response that would be effective and overwhelming.
“North Korea continues to launch missiles, develop its nuclear weapons programme and engage in threatening rhetoric and behaviour.”
Kim Jong-Un in pictures Mon, January 23, 2017
Kim Jong-Un, The Supreme Leader of North Korea takes himself and his leadership very seriously.
Play slideshow AFP/Getty Images 1 of 62
North Korean leader Kim Jong-Un paying his final respects at the bier of Kang Ki Sop, alternate member of the Central Committee of the Workers' Party of Korea, deputy to the Supreme People's Assembly of the DPRK and general director of the General Administration of Civil Aviation, following Kang's death at an undisclosed location in North Korea.
The defence secretary’s words came after North Korean leader Kim Jong-un said in his New Year speech his army was close to test-launching an intercontinental ballistic missile – and state media has said a launch could come at any time.
North Korea conducted its fifth test of a nuclear device last year and was seen by experts and officials to be making progress in its weapons capabilities.
Last month, South Korean defence minister Han Min-Koo warned Kim’s nuclear and missile provocations are a “direct and realistic” threat to South Korea.
He said: “North Korea is making threats of nuclear development and intercontinental ballistic missiles this year as well.
“Pyongyang’s missile threat against the Seoul metropolitan area where key facilities and population are concentrated is directly linked to the nation’s security.
“Thus, there should be no weak point in preparation.”
- Nigel Farage hammers raging LBC caller over Bercow Trump comments
- Kim Jong-un WILL BLAST Trump in '9/11 size attack', expert fears
- US Navy OBLITERATES missile in new weapons defence system test