In the first visit by a US defence secretary in nearly four years, Hagel flew from Kabul to Islamabad to meet Prime Minister Nawaz Sharif and other top officials, including the country's new army chief.
Ties between Washington and Islamabad have been seriously strained over US drone strikes in Pakistan's tribal belt as well as Afghan Taliban sanctuaries inside Pakistan's borders.
Hagel visited "in recognition of the tremendous support that Pakistan has provided in the war on terror," a senior US defence official told reporters before his arrival.
The defence secretary wants "to deepen our defence partnership" and to affirm continued US military assistance, the official said.
"There is some friction in the relationship" and Hagel wants to tackle that "head on" to try to forge a better understanding between the two countries, he said.
The visit came as Hagel's deputies withdrew a statement issued late Sunday that said NATO shipments out of Afghanistan through Pakistan were to resume due to the end of anti-drone protests.
In recent weeks, activists opposed to the drone raids forcibly searched trucks in northwest Pakistan in a campaign to disrupt NATO supply routes to and from Afghanistan.
The club-wielding protesters have prompted US officials to halt the shipments to protect the safety of truck drivers ferrying NATO equipment.
Contractors were still concerned over anti-drone protests and the suspension had not been lifted, officials travelling with Hagel told reporters.
The crossing is the main overland route used by the Americans and NATO to withdraw tonnes of military hardware from Afghanistan as part of a massive troop pullout set to wrap up by the end of 2014.
President Barack Obama has defended the drone strikes as an effective, lawful tool used with restraint to target suspected Al-Qaeda militants. But human rights groups and Pakistani politicians say the missile attacks have killed innocent civilians and must stop.
US officials are anxious to forge a constructive dialogue with the new army chief General Raheel Sharif, who is expected to be at the centre of decision making on sensitive security questions.
The veteran infantry commander last month succeeded General Ashfaq Kayani, who is retiring after six years at the helm.
Hagel's spokesman said the defence secretary looked forward to discussing with his counterparts "the United States and Pakistan's common interest in a stable Afghanistan".
Pakistan is seen as crucial to peace in neighbouring Afghanistan as it was a key backer of the hardline 1996-2001 Taliban regime in Kabul and is believed to shelter some of the movement's leaders.
Pakistan is battling a homegrown Islamist insurgency but US officials have long accused Islamabad's spy service of maintaining ties to the Afghan Taliban, as a hedge to counter any potential threat from India in neighbouring Afghanistan.
Hagel landed in Pakistan after two days in Afghanistan, where he urged the country's president, Hamid Karzai, to sign a long-delayed security agreement that will allow NATO-led forces to stay in the country after 2014.
Hagel began his trip last week in Bahrain, seeking to reassure Gulf allies that the United States would retain a robust military presence in the region despite an interim nuclear deal with Iran.
After morning meetings in Pakistan, Hagel was due to travel to Saudi Arabia and Qatar, where he was expected to renew his message of solidarity with the Gulf Arab states.
The Saudis in particular are wary of the diplomatic opening with Tehran as they view Shiite-led Iran as a regional rival.