The THAAD system "is operational and has the ability to intercept North Korean missiles and defend the Republic of Korea", a spokesman for US Forces Korea said in a statement.
THAAD was deployed to South Korea by the US in response to North Korea's increased missile and nuclear tests, but the defence system has drawn sharp opposition from China and Russia as their territories are within the system's range, CNN reported.
China again expressed its displeasure on Tuesday, urging both sides to "stop the deployment immediately".
"We will also firmly take necessary measures to safeguard our own interests," said Chinese Foreign Ministry spokesman Geng Shuang.
The system may have been deployed, but according to a US defence official, its operation is "limited".
Nevertheless, the US official said the system is capable of shooting down a North Korean missile, adding that the US hopes to install additional units to increase coverage over South Korea.
The anti-missile system is not expected to be fully operational until the end of the year, according to the report.
"These things are now in place, so you can connect them to get the operational capability from early on -- that's what 'within days' means," he said.
Moon Jae-in, the frontrunner in South Korea's presidential election which will take place on May 9, expressed scepticism over THAAD.
Speaking to South Korean radio station BBS FM on Tuesday, Moon said the deployment was "not a done deal yet", and should be based on public consultation and a vote in the country's National Assembly.
THAAD is designed to shoot down short- and medium-range ballistic missiles in the latter stages of their flight as they plunge towards their targets.
It also includes a sophisticated radar that will fit into an overlapping series of US missile defence systems, including Aegis warships operating in the Pacific and Patriot missile batteries deployed in Japan.