The Seoul Central Prosecutors' Office said the private was accused of raping the 18-year-old in September after breaking into her room in Seoul.
The soldier had allegedly taken the girl home after they drank together overnight with two companions, before returning to her room later and raping her.
He has reportedly denied the charges, but prosecutors arrested him after securing DNA evidence.
On November 1, a court jailed another US soldier for 10 years for raping a 18-year-old girl multiple times in Dongducheon city, which hosts the US Second Infantry Division base and is close to the border with North Korea.
During his visit to Seoul in October, US Assistant Secretary of State Kurt Campbell offered an apology to the Korean people for "the tragic and inexcusable rape".
The US military also apologised and imposed a month-long late-night curfew on its troops in the country.
Crimes by the 28,500 US troops based in the South are a sensitive subject, even though many see their presence as necessary to deter a North Korean attack.
Major anti-American protests broke out after a US armoured vehicle killed two schoolgirls in a traffic accident in 2002.
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