Clinton arrived with Adm. Mike Mullen, chairman of the U.S. Joint Chiefs of Staff, for a seven-hour trip and met with Pakistan's president and other officials.
It's the first high-profile American visit since the raid that killed bin Laden, which has added to the tension between the two countries.
While Clinton said the U.S. maintains its support and commitment to work with Pakistan, she also criticized Pakistanis for propagating conspiracy theories and anti-American sentiment.
Pakistani officials are angry they were not told in advance of the bin Laden raid, who was living in an army town not far from the capital, Islamabad. Parliament has passed resolutions condemning the U.S. incursion, and the U.S. has been asked to reduce the number of military personnel it has stationed in nuclear-armed Pakistan, which has become a nexus for Islamic extremism.
In the U.S., suspicions have abounded that elements in Pakistan's security services may have harbored the terrorist mastermind, and some lawmakers have called for a review of the billions in military and humanitarian aid that the U.S. gives to Pakistan.
After the meeting, Clinton said relations "had reached a turning point," but that she thought Pakistan knew the stakes involved. She joked about the tense atmosphere witnessed by reporters at the beginning of the talks, but was serious-faced for the most of the news conference.
The Associated Press contributed to this report.