The country, once the home of President Obama, is the second stop in her inaugural overseas trip as the top U.S. diplomat. The itinerary is intended to symbolize the administration's commitment to Asia.
In Jakarta, Clinton intends to announce plans to step up U.S. engagement with Southeast Asia in particular, stressing the growing importance of a region that often felt slighted by the Bush administration.
Her two-day schedule in Indonesia includes a visit to the Southeast Asian Nations (ASEAN) secretariat, the first by a secretary of state, where she is likely to signal U.S. intent to sign the regional bloc's Treaty of Amity and Cooperation, officials said.
Jakarta is not typically a stopping point for American officials, reports CBS News correspondent Wyatt Andrews, traveling with Clinton. But, the White House is seeking to exploit the President's connections to Indonesia - the world's largest majority-Muslim country, which also happens to be a growing, stable democracy - to deliver a message of reconciliation.
Clinton also plans to pledge to attend the group's annual regional security conference, they said. Former Secretary of State Condoleezza Rice skipped the ASEAN Regional Forum twice during her four years in office, to the dismay of the region.
In addition, Clinton hopes to announce the resumption of Peace Corps operations in Indonesia after a more-than-40-year absence, the officials said. Peace Corps volunteers served in the country between 1963 and 1965 before being expelled by the government.
Andrews reports that Clinton also plans to discuss human rights, trade, and the issue of deforestation. The U.S. wants to find new ways to stop illegal logging in Indonesia, because the loss of rain forest here is believed to be a major global source of greenhouse gasses.
Indonesian leaders say they also hope to discuss the Iranian nuclear dispute and the war in Afghanistan.
Obama spent four years of his childhood in Indonesia. Among those who turned out at the airport to welcome Clinton were 44 children from his former elementary school, singing traditional folk songs and waving Indonesian and U.S. flags.
Indonesia, often held up as a beacon of Islamic democracy and modernity, is a secular nation. Most of its 190 million Muslims practice a moderate form of the faith, but public anger ran high over U.S. policy in the Middle East and the invasions of Iraq and Afghanistan during the Bush years, fueling a small but increasingly vocal fundamentalist fringe.
The militant group Jemaah Islamiyah has carried out a series of suicide bombings targeting Western interests in Indonesia since 2002, killing more than 240 people, many of them foreign tourists. But experts say a police crackdown has severely weakened the movement; the last attack occurred more than three years ago.
U.S. officials said Clinton is keen to show Washington's appreciation for Jakarta's counter-terrorism efforts, particularly in combatting Jemaah Islamiyah.
Security was tight for Clinton's visit, with 2,800 police being deployed in Jakarta along with members of the army, according to local police. Witnesses saw scattered protests in and around the capital, but no arrests or injuries were reported.
Outside the presidential palace in Jakarta, about 40 Muslim students from various universities rallied against Clinton. Some threw shoes a caricature of Clinton, screaming "Hillary is terrorist." Others unfurled banners saying "Chase Hillary away" and "America, destroyer of cultures."
During Clinton's first Asia stop, in Japan, her two days of talks, and on the global financial crisis. After Indonesia, she travels to South Korea and China, where North Korea is again likely to dominate her meetings.
In Tokyo on Tuesday, though, Clinton previewed a new approach to dialogue she will try out in Indonesia and other nations. During a town hall student meeting, she said the United States was under new management.
"America is ready to listen again," she said. "Too often in the recent past, our government has not heard the different perspectives of people around the world. In the Obama administration, we intend to change that."
Later, in response to a student question about the Bush administration's perceived "prejudice" against Muslims in the war on terrorism, Clinton lamented that America's failure to communicate its intentions with the world is "one of the central security challenges we face."
She also acknowledged that the task had gotten harder because of the hugely unpopular war in Iraq, which she initially supported as a senator, but came to oppose. That conflict, she said, was "viewed as wrong by many in the world."
"I think that the war on Iraq made our argument more difficult," Clinton said.
Still, she stressed, the administration would not shy from the topic.
"I think you will see from President Obama and those of us in his administration a concerted effort to present a different position to the Islamic world without in any way stopping our efforts to prevent terrorism," Clinton said.