The duo - part of the advance team ahead of President Joe Biden's visit to the country - were bar-hopping in Seoul on Thursday night, US media reports.
One of the employees is said to have got into a physical altercation with a local taxi driver.
No one was detained or arrested but Seoul police investigated the incident.
The agency "is aware of an off-duty incident involving two employees which may constitute potential policy violations", Anthony Guglielmi, a Secret Service spokesman, said in a statement.
He said both employees have been placed on administrative leave and their absence will have no impact on Mr Biden's trip.
The president's trip to Seoul is the first leg of a four-day swing through Asia amid growing concern over sabre-rattling in the region by China and North Korea.
Sources confirmed to the BBC's US partner CBS News that the Secret Service pair - a special agent and a security specialist - were sent home on Friday afternoon, barely an hour before the president's official arrival in the South Korean capital.
According to CBS, the administration will investigate whether they were intoxicated at the time of the incident, rather than the incident itself.
It is unclear how the altercation with the taxi driver began.
The employees were returning to the Grand Hyatt Hotel after their night out when the incident took place.
Local police, hotel security and two other individuals are said to have been involved.
Seoul police investigated one of the Secret Service employees and interviewed the other parties but decided not to make an arrest or file charges.
-- Courtesy of BBC News