It marks the first arrest warrant issuance after the abrupt imposition of martial law on the night of Dec. 3.
The judge acknowledged that there was a risk of Kim destroying evidence and recognized him as a flight risk.
Prosecutors requested the arrest warrant against Kim on Monday evening, accusing him of taking key actions in an insurrection and power abuse. Kim is suspected of preparing the martial law decree and ordering a raid by martial law forces into the parliament.
In an application for the arrest warrant, prosecutors wrote that "Kim conspired with Yoon and instigated a riot with the purpose of harming the Constitution," according to Yonhap News Agency.
Kim reportedly said that sending 280 armored soldiers into the National Assembly was a decision to enforce the martial law decree. Kim also told the special investigation bureau of the Supreme Prosecutors' Office that he wrote the decree by himself and "confirmed the wordings in the decree after consulting with Yoon."
Kim is also suspected of tampering with evidence as he used three mobile devices after martial law was lifted in the early hours on Dec. 4.
According to telecommunication records obtained by Rep. Hwang Jung-a from the liberal Democratic Party, Kim activated the new phone last Thursday afternoon and switched his SIM card again. A day after, on Dec. 6, Kim allegedly activated another mobile device and inserted his SIM card.
In the early hours Sunday, Kim voluntarily appeared at the Seoul Central District Prosecutors' Office in southern Seoul.