The Seoul Central District Court issued an arrest warrant for Lee early Friday.
South Korean prosecutors are attempting for a second time to arrest Samsung's de facto leader, who is being investigated on bribery allegations in connection with a massive political scandal.
With Lee facing a formal arrest, the group's Future Strategy Office, which supervises Samsung's groupwide business decisions, is expected to play a key role in making decisions.
A Seoul court said on Tuesday it would hold a hearing on the request for arrest warrants at 10:30 a.m. (0130 GMT) on Thursday.
Lee has been accused of bribing the suspended South Korean president, Park Geun-hye.
If the court approves the warrant, prosecutors will be able to take him into custody for up to 21 days before formally pressing charges.
Park has been stripped of her powers while the Constitutional Court decides whether to uphold her impeachment.
The court's rejection last month of the arrest request dealt a blow to the prosecutors, who have until February 28 to investigate unless parliament extends the deadline.
"If he is arrested, it would be a huge event that could end a deep-seated evil in South Korean society: the collusion between the government and businesses". "If the arrest is dismissed, it would mean a sabotaging of the investigation by the judiciary". Some planned to stay all night.
In January, the court rejected the prosecution's request for an arrest warrant for Lee. In 2008, Lee's father, Lee Kun-hee, and three other senior Samsung executives were indicted on charges of financial wrongdoing. The trappings of the scandal have garnered global attention for their freakish details: Choi claims to be channeling the spirit of Park's dead mother and allegedly is the power behind the throne.
Lee was also accused of embezzlement, perjury and allowing the group to buy two pricey horses for the daughter of Choi. The implication is that the payments were made to smooth the regulatory process for transferring Samsung's ownership from father to son. According to JoonAng Daily, the National Pension Service also happened to be the largest shareholder of Samsung C&T - and the deal was criticized as unfair for Samsung C&T.
The merger strengthened the Lee family's control over Samsung.
They are also seeking the arrest of the president of Samsung Electronics Co Ltd, Park Sang-jin, who also heads the Korea Equestrian Federation and attended Thursday's hearing with Lee. Though the ailing Samsung chair was convicted before, the 75-year-old has never spent time in prison. After his latest conviction in 2008, he was pardoned a year later by the president, who said he would help South Korea's bid to host the 2018 Winter Olympics.