Kerry, who has emerged a key US emissary in times of crisis, held talks with Kayani late on Sunday night and met President Asif Ali Zardari and Prime Minister Yousuf Raza Gilani on Monday.
The chairman of the Senate Foreign Relations Committee is the first senior US official to visit Pakistan since bin Laden was killed in the garrison city of Abbottabad on May 2.
Kayani "apprised the visiting dignitary about intense feelings of the rank and file of Pakistan army on the Abbotabad incident", said a statement issued by the military on Monday.
The two leaders decided to hold detailed discussions on Pakistan-US relations during meetings with the civilian leadership of the country, the statement said.
Observers said Kerry was likely to have pressed Pakistan's leadership to demonstrate their commitment to the campaign against Al Qaeda and the Taliban against the backdrop of questions raised by bin Laden's presence in a city that is home to thousands of soldiers.
Shortly after Kerry flew into Islamabad from Afghanistan on Sunday, US Secretary of State Hillary Clinton telephoned President Asif Ali Zardari and discussed the situation in the aftermath of the killing of bin Laden.
Clinton and Zardari "agreed to resolve issues amicably and move forward", said a statement from the presidency.
Zardari apprised Clinton of "concerns expressed by Pakistan's parliament over the US operation".
Pakistan has condemned the US raid against bin Laden as a violation of its sovereignty and warned that it will retaliate with "full force" against any similar operation.
The attack sparked widespread anger in Pakistan and a special in-camera parliamentary session on Friday too condemned the US raid.
Referring to bin Laden's presence in a compound a short distance from an elite military facility, Central Intelligence Agency chief Leon Panetta said that Pakistani authorities were either complicit or incompetent.
Kerry arrived in Islamabad after a two-day visit to Afghanistan.
The US media has reported that Kerry is carrying a list of actions that Pakistan can take to ease tensions.
A senior American official was quoted as saying that the US would try to use the threat of Congressional cuts to annual aid to Pakistan as leverage.
Kerry told mediapersons in Mazar-e-Sharif on Saturday that attacks in Afghanistan are carried out by militants trained in Pakistan.
He said Pakistan should act honestly in the fight against terrorism.
"It is really critical that we talk with the Pakistanis, as friends, in the best effort to try to achieve the most cooperation possible to make all of us safer. We believe that Pakistan itself is challenged from these insurgents, extremists and terrorists," Kerry told reporters ahead of his visit to Islamabad.
Kerry played a key role in efforts to resolve the crisis in Pakistan-US relations following the arrest of CIA contractor Raymond Davis in Lahore in January.
Davis, who was arrested after he shot dead two Pakistanis, was freed in March after over $2 million was paid to the families of the dead men under a "blood money" deal.
Image: Pakistan PM Gilani meets US Senator Kerry in Islamabad on Monday
Photograph: Mian Khursheed/Reuters
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