The missiles fired from the Sino-ri base in the north-west of the country travelled 420km (260 miles) and 270km.
The tests come as a top US envoy is in South Korea for talks on how to break the deadlock over nuclear negotiations.
Analysts say the North is trying to increase pressure on the US over its failure to make concessions.
A meeting in Vietnam between North Korean leader Kim Jong-un and US President Donald Trump ended without agreement in February. Mr Trump walked away from what he described as a bad deal offered by Mr Kim.
What do we know about the latest firing?
The two missiles were fired towards the east at about 16:30 local time (07:30 GMT), South Korea’s Joint Chiefs of Staff said in a statement.
Detailed analysis was being carried out in co-operation with US intelligence officials, it added. There were no details of where the missiles landed.
Located some 75km from the capital, Pyongyang, the Sino-ri base is one of North Korea’s longest-running missile facilities, according to the Washington-based think-tank Center for Strategic and International Studies.
On Saturday, the North tested several short-range missiles from the eastern Hodo peninsula, according to South Korea.
The missile launch, the first since Pyongyang tested an intercontinental ballistic missile in November 2017, came after the country tested what it described as a new “tactical guided weapon” last month.
What about the nuclear impasse?
Hours earlier, US Special Representative on North Korea Stephen Biegun arrived in the South Korean capital, Seoul, to discuss ways of getting denuclearisation talks back on track.
He is expected to discuss ways to provide humanitarian food aid to North Korea amid reports that it had suffered its worst harvest in decades, leading to chronic food shortages.
Tensions have risen between the countries since their summit in Vietnam broke down, with the US insisting North Korea give up its nuclear programme and Pyongyang demanding sanctions relief.
Last year, Mr Kim said he would stop nuclear testing and would no longer launch intercontinental ballistic missiles.
Nuclear activity appears to be continuing, however, and satellite images of North Korea’s main nuclear site last month showed movement, suggesting the country could be reprocessing radioactive material into bomb fuel.
The country claims it has developed a nuclear bomb small enough to fit on a long-range missile, as well as ballistic missiles that could potentially reach the US mainland.
Meanwhile, the US has halted efforts to retrieve the remains of its troops killed during the 1950-1953 Korean War amid a breakdown in communications following their failed summit.