Admiral Mike Mullen's trip follows a visit to Afghanistan a day earlier in which he told reporters he would raise ongoing concerns with Pak army chief General Ashfaq Kayani, according to the Joint Chiefs of Staff website.
Mullen praised cooperation between US and Pakistani troops in working jointly to combat the militant Haqqani network who target Nato forces in the Afghan east.
"Haqqani is having a much more difficult time now," Mullen told reporters, according to an article on the website.
"All that said, we're still working through the (Pakistani) military support, the way through the relationships the (Pakistani intelligence agency) has with the Haqqani network, and the strain that creates."
Mullen's trip is the latest shuttle diplomacy mission after a fatal shooting by a CIA contractor in January enflamed a row between the US and Pakistan over intelligence sharing and raised tensions over the controversial US drone war.
"We're going to have a very tough year this year," he told reporters.
"I've been very straight with the American people on that. I think our losses, which were significant last year, will be significant this year as well."