In a speech, President Park Geun-Hye said she was aware of the "gruesome realities" North Koreans face daily.
"We will keep the road open for you to find hope and live a new life," she said. "Please come to the bosom of freedom in the South."
Her comments come after a North Korean soldier crossed the heavily-protected Demilitarized Zone to the South.
"The universal values of freedom, democracy, human rights and welfare are the precious rights you should also enjoy," she said in a speech to mark the country's armed forces day.
She also issued a warning to Pyongyang about its nuclear tests, saying South Korea would defend itself.
Media outlets in North Korea are controlled by the authoritarian state, and it is unclear whether Ms Park's invitation will reach many citizens.
The heavily-policed border between North and South Korea has been in place since the end of the Korean war in 1953.
The Demilitarized Zone (DMZ) is 4km (2.5 miles) wide, stretching across the border, and is fortified by landmines, barbed wire, and policed by thousands of soldiers.
Defection across the DMZ is very rare. Thursday's incident was the first such crossing in more than a year.
A similar defection happened in 2015, when a teenage recruit presented himself to South Korean soldiers at the border.
Before that, the last defection across the DMZ had been in 2012, when a soldier from the North handed himself over after passing surveillance cameras and electric fences, in an incident which prompted a major security review.
Seoul says almost 30,000 North Koreans have defected since the 1950s, but most of them do so through China.
They receive some government help integrating, although some still complain of financial difficulties and discrimination.
Tensions between North and South Korea remain high, as Pyongyang continues a series of nuclear bomb tests in the face of international sanctions.