Her arrival on Saturday coincided with the start of major annual US-South Korean military exercises that North Korea says are a prelude to an invasion.
Rice, on the fifth leg of her first Asian tour since taking office, arrived at a military airbase in southern Seoul and flew by helicopter to a nearby bunker that is the command post for the exercises.
About 17,000 US troops, 6000 of them stationed in South Korea, are taking part in the annual exercise with an unspecified number of South Korean troops.
"Thank you for what you do every day in the front line of freedom," Rice told about 300 people including US and South Korean soldiers at the bunker.
She said that although the Cold War had ended in other parts of the world, divisions remain on the Korean peninsula.
"I know that you face a constant threat every day. (South Korea) faces a threat ... from a state that is not democratic, that is not free, and doesn't have the best interest of its people at heart," she said.
About 17,000 US troops are
taking part in an annual exercise
"The forward march of freedom continues because of the strength of people, the men and women of the US forces in Korea and of the Republic of Korea (South Korea)."
Rice is the highest US official to have visited the top-security command post code-named Tango, according to US officials.
The aircraft carrier USS Kitty Hawk and its battle group arrived at the southeastern port of Busan a week before the drills with 5200 sailors and 60 aircraft, including F-18 Super Hornets.
A Striker unit - a rapid task force with armoured vehicles - is also taking part.
"The level of the US troops and military equipment mobilised this time is similar to ones in the preceding years," the US military command in Seoul said in a statement.
The drill focuses on a mock battle aimed at evaluating command capabilities to receive US forces from abroad, with troops mobilised for anti-commando operations and computer war games.
The United States says the exercise is "defence-oriented" and designed to improve the ability of allied forces to defend South Korea against external aggression.
North Korea's reaction
But North Korea has reacted nervously.
"The projected exercises are extremely dangerous nuclear war drills to mount a preemptive attack on the DPRK (North Korea)," the official Korean Central News Agency said on Friday.
"The DPRK will take all the necessary countermeasures including the increase of its nuclear arsenal to cope with the extremely hostile attempt of the US to bring down its system chosen by the Korean people themselves," it said.
"The projected exercises are extremely dangerous nuclear war drills to mount a preemptive attack on the DPRK (North Korea),"
Korean Central News Agency
The country's "nukes serve as powerful deterrent to keep the balance of forces in Northeast Asia, prevent the outbreak of a new war and preserve peace," it said.
Rice arrived from Japan for a two-day visit expected to focus on the North Korean nuclear issue. She is scheduled to meet President Roh Moo-Hyun, Unification Minister Chung Dong-Young and Foreign Minister Ban Ki-Moon on Sunday.