The South Korean Defense Ministry said the Terminal High Altitude Area Defense (THAAD) would be deployed in the southeastern county of Seongju to maximize its effectiveness while minimizing any impact on residents and the environment.
"By operating the US THAAD battery in Seongju, we will be able to better protect one half to two-thirds of our citizens from North Korean nuclear and missile threats," the ministry said in a statement, Reuters reported.
"It will dramatically strengthen the military capabilities and readiness to defend critical national infrastructure such as nuclear power plants and oil storage facilities, as well as the military forces of the South Korea-US alliance."
South Korea and the United States said last Friday they had made a final decision to deploy the THAAD system in the South.
North Korea's military on Monday threatened to retaliate against the deployment of the system with a "physical response" once its location and time of installation were decided.
South Korea's Defense Ministry has said it aims to have the system operational by the end of 2017.
China worries the system's radar will be able to track its military capabilities and would destabilize the regional security balance. Russia also opposes the deployment.
Seongju is a town of 45,000 people, many of them grow yellow melons for a living. South Korean media reported the THAAD system will be placed on a mountain where a South Korea air defense artillery unit is based. About 200 Seongju residents made a protest visit to Seoul's Defense Ministry on Wednesday.
There have been protests about the system's location, with residents fearing harmful economic and environmental effects.
Thousands took to the streets Wednesday in Seongju town, carrying banners reading "We absolutely oppose THAAD deployment", Yonhap news agency reported.