Clinton's two-day visit will include talks with top military and civilian leaders as well as pledges of economic aid which Washington hopes will demonstrate to a skeptical public that the United States is a trustworthy partner in the struggle against Taleban insurgents on both sides of the Afghanistan-Pakistan border.
US officials kept details of Clinton's visit secret prior to her arrival amid sharp security concerns following a wave of suicide bombings and militant attacks in Pakistan itself.
One day before she arrived, suspected militants in a tribal region on the Afghan border ambushed a convoy of vehicles being escorted by security forces, killing 18 people.
Security will be equally tight during her next stop in Afghanistan, where she will take part in an international conference on Tuesday as the US-led war effort runs into mounting doubts in the US Congress.
The conference is aimed at fleshing out Afghan President Hamid Karzai's pledge to assume more responsibility for both security and governance ahead of US President Barack Obama's July 2011 target date to begin drawing down US forces.
History of mistrust
The Obama administration sees nuclear-armed Pakistan as a pivotal player in the struggle against militant Islamist groups in both countries, but the two sides are divided by a history of distrust and sometimes diverging goals over a war that is increasingly unpopular.
Public opinion polls have shown many Pakistanis doubtful about long-term US intentions, citing examples of abandonment particularly after the Soviets withdrew from Afghanistan.
US officials, meanwhile, are wary of the role that Pakistan is playing in Afghanistan and believe it needs to do more to fight its own homegrown Taleban militants, which Washington blames for the attempted bombing in New York's Times Square on May 1.
Richard Holbrooke, the Obama administration's special representative for Afghanistan and Pakistan, said there was a "dramatic acceleration" in cooperation between the two governments, but conceded Pakistani public opinion was lagging.
"We only have small indications of improvement in the polls, but significant examples of improvements in the government," Holbrooke told reporters in Islamabad, adding Pakistan's own fragile political structure was also stabilising.
"This change is of strategic importance because it's enabling us to move forward in our additional efforts on counter-terrorism," he said.
Clinton's meetings with Pakistan President Asif Ali Zardari and military chief General Ashfaq Kayani build on talks held in Washington in March aimed at speeding the flow of both security information and billions of dollars in US aid.
US officials hope shows of US help on everything from water and power projects to womens rights will turn public opinion in Pakistan, where polls show fewer than one in five Pakistanis view the United States favorably despite a tripling of civilian aid to $7.5 billion in the next five years.
Clinton has often expressed a deep personal affection for Pakistan and is expected to wield her own charisma in the effort to win support, appearing at several public engagements where she can pitch the U.S case to local audiences who were widely hostile during her last visit in October.
