Kayani, who is on a two-day bilateral visit to Jordan, met Kerry in Amman last night.
"Both (leaders) discussed the reconciliation process in Afghanistan and security issues concerning the South Asian region," the spokesman said without giving details.
This was the first meeting between the two leaders since Kerry was appointed the Secretary of State.
However, Kerry is perceived as being close to Pakistan's top military leadership, especially Kayani.
Pakistan has been pushing for a greater role in the peace and reconciliation process in Afghanistan ahead of the withdrawal of US and foreign troops in 2014.
Despite the release of 26 Afghan Taliban leaders last year, Pakistan has been unable to make headway in its efforts to take forward the reconciliation process in Afghanistan.
In the past, Kerry has played a key role in the Obama administration's efforts to address sensitive issues with the Pakistani military.
In February 2011, Kerry helped broker a deal to free Raymond Davis, a CIA contractor who was arrested in Lahore after he shot and killed two Pakistani men who were linked to an intelligence agency.
Following negotiations between Kerry and Pakistani leaders, Davis was released after millions of dollars were paid as "blood money" to the families of the dead men.
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