President Yoon Suk Yeol has been placed under pretrial detention over his botched martial law bid last month.
The Seoul Western District Court issued the warrant early on Sunday following an hourslong deliberation, citing concerns about the destruction of evidence.
It marks the first time in South Korea's constitutional history for a sitting president to be placed under pretrial detention.
Yoon, who has been in detention since his arrest on Wednesday at his presidential residence, is facing charges of insurrection in connection with his short-lived martial law imposition on December 3.
With the warrant, investigators can keep Yoon in custody for up to 20 days, including the days he has already spent at a detention center.
The Corruption Investigation Office for High-ranking Officials, which has no authority to indict, is expected to transfer Yoon's case to the prosecution around Friday for indictment.
The prosecution is then likely to investigate him further and indict him around February 5.