Yoon is the first sitting president of South Korea to face arrest.
Investigators have until Jan. 6 to execute the warrant and can request an extension.
However, it is unclear whether investigators will be able to execute the warrant as they may be hindered by his security team and protesters.
The Presidential Security Service previously blocked investigators from entering the presidential office and Yun’s private residence to conduct court-sanctioned searches.
In the past, South Korean authorities have abandoned attempts to arrest prominent politicians after their aides and supporters physically blocked police.
On Monday, Yun’s legal team said investigators did not have the authority to arrest him because declaring martial law is within the president’s constitutional authority.
Yun previously defended his decision to declare martial law and promised to “fight to the end” – although he also said that he will not avoid legal and political responsibility.
His lawyer Yoon Gap Geun said Yoon’s refusal to comply with the three previous subpoenas was due to “legitimate concerns.”
Yoon’s whereabouts are unknown, but he is banned from leaving the country.
Although he has been suspended from presidential duties since December 14 after lawmakers voted to impeach him, he can only be removed from office if his impeachment is upheld by the country’s constitutional court.
Currently, there are only six judges in the nine-member Constitutional Court. This means that one refusal will save Yoon from removal.
Opposition lawmakers had hoped the appointment of three additional judges would improve the chances of Yun being impeached, but Prime Minister Han Dak-soo vetoed their proposal last week.
The opposition has since voted to impeach Khan, who stepped in as acting leader after Yoon was suspended.
Now they are threatening to do the same to Finance Minister Choi Sang-mok, who currently serves as president and prime minister.
Additional reporting by Kelly Ng
