Yoon is under criminal investigation for his short-lived martial law attempt on December 3.
An arrest would be unprecedented for an incumbent South Korean president.
Supporters of President Yoon have gathered with outside the presidential residence. (EPA PHOTO)
Yonhap reported that officials from the Corruption Investigation Office for High-ranking Officials (CIO), which is leading a joint team of investigators that include the police and prosecutors, had left their headquarters to execute the warrant.
Broadcaster YTN reported that about 2800 police had been mobilised in preparation for executing the warrant.
It was unclear exactly how police would make the arrest and whether the Presidential Security Service, which has blocked access by investigators with a search warrant to Yoon's office and official residence, would try to stop it.
About 100 protesters were gathered in the pre-dawn hours near his residence on Friday, amid local media reports that investigating authorities would soon try to execute an arrest warrant that was approved on Tuesday after Yoon refused summons to appear.
"We have to block them with our lives," one was heard saying to others. About a dozen protesters tried to block a group of police officers at the entrance to a pedestrian overpass.
Yoon sent shockwaves through the country with a late-night announcement on December 3 that he was imposing martial law to overcome political deadlock and root out "anti-state forces".
Within hours, however, 190 MPs had defied the cordons of troops and police to vote against Yoon's order. About six hours after his initial decree, Yoon rescinded it.
He later issued a defiant defence of his decision, saying domestic political opponents are sympathetic to North Korea and citing uncorroborated claims of election tampering.
Yoon has been isolated since he was impeached and suspended from power on December14.
Separate from the criminal investigation, his impeachment case is currently before the Constitutional Court to decide whether to reinstate or permanently remove him.
A second hearing in that case is scheduled for later on Friday.
