Calling Egypt "critical to the peace and security" of the region, Kerry said the U.S. wants to help Egypt succeed in its efforts to overcome the "difficult challenges" it faces economically and in combatting extremists in the Sinai Peninsula, where militants have formed a local ISIS affiliate.
Kerry promised to return to Cairo with ideas to help invigorate Egypt's economy and to aid Egypt in its campaign against ISIS.
"We talked about ways in which we can hopefully resolve some of the differences and questions that have arisen about the internal politics and choices for the people of Egypt," Kerry added.
It was an oblique reference to the deteriorating human rights situation that has been a source of growing tensions between the longtime allies and has triggered a debate in Washington about U.S. economic assistance.
The Obama administration has become increasingly public with its frustrations as the government crackdown on civil society has intensified.
Last month Kerry said he was "deeply concerned" about the worsening democratic trends in Egypt, including the government's decision to revive an investigation into two prominent human rights activists whose NGOs are accused of illegally receiving foreign funding.
The decision, Kerry said, came against "a wider backdrop of arrests and intimidation of political opposition, journalists, civil society activists and cultural figures."
The comments drew a sharp response from Egyptian Foreign Minister Sameh Shoukry, who said Egypt rejected "tutelage" about its human rights from other countries.
But Shoukry was far more upbeat Wednesday, saying the talks with Kerry were "cordial and productive" and "addressed both of our desires to put this relationship on an upward trajectory."
"Egypt greatly values U.S. assistance (and) is glad the U.S. seeks to continue its support at a critical time," Shoukry told CNN.
Shoukry said Kerry and el-Sisi discussed the political climate in Egypt and "ways how to best create an atmosphere that helps Egypt prosper economically, but with a recognition of the dangers Egypt faces and its need to create stability."
U.S. officials and lawmakers say without serious improvement in the human rights situation in Egypt, America may be forced to rethink some of its economic aid.
The $150 million a year in economic assistance the U.S. gives to Egypt is at stake, as well as a backlog of hundreds of millions of dollar in funding for programs to strengthen democracy and promote economic development that was appropriated by Congress but has yet to be delivered.
Officials and lawmakers say the Egyptian government's crackdown on civil society and restrictions on NGOs are making it increasingly difficult, if not impossible, to implement the programs.
"The Egyptian government has been closing the space for alternative points of view and using threats and imprisonment to prevent civil society from functioning," said Democratic Sen. Patrick Leahy, the ranking member of the State Department and Foreign Operations Subcommittee on Appropriations. "It leaves the U.S. with few options."
Leahy, who recently wrote Kerry asking him to investigate "gross violations of human rights" by Egyptian forces, is leading a growing chorus of voices in Congress that argue the Economic Support Funds allocated for Egypt should be re-assigned to other countries because of the government's lack of support for the programs.
"The el-Sisi government is going in the wrong direction by cracking down on journalists, outlawing NGOs and imprisoning political opponents," Leahy told CNN. "If we can't find ways to carry out assistance programs in Egypt, there are plenty of other countries whose governments are better partners where we can use the funds effectively."
Shoukry said "bureaucratic hurdles" have posed challenges regarding the aid, but that Kerry and el-Sisi discussed ways to overcome them and said the Egyptian government was committed to doing so.
But Eric Trager, a fellow at the Washington Institute for Near East Policy, believes U.S. economic aid raises Egyptian suspicions over foreign funding that strike at the regime's own survival.
"This regime is incapable of political reform because views it as suicidal. This government believes all political turmoil is a foreign conspiracy driven by foreign funding, not driven by something organic within Egyptian society," Trager said.
The debate over Egypt's aid reflects a long-standing tension between U.S. security interests in stable, friendly countries and the desire to promote core American values such as freedom of speech and worship.
That friction is particularly acute in the Middle East, where the Obama administration has shifted from idealism to realpolitik since the so-called Arab Spring has devolved into a protracted, bloody conflict across the region.
Despite the discussion over whether to cut some of the economic assistance, the administration and Congress remain steadfastly committed to the $1.3 billion in U.S. military aid to Cairo.
In 2013, Washington suspended military aid to Egypt to push the new military regime, led by el-Sisi, to improve its democratic track record. That move came after months of internal administration debate over whether to label the military overthrow of President Mohamed Morsi of the Muslim Brotherhood a coup.
In February, Kerry asked Congress to waive all human rights restrictions that apply to the annual military aid to Cairo, prioritizing Egypt's strategic importance to the U.S. and difficult security environment over what he admitted where "distributing" trends on the human rights front.
Republican Sen. Lindsey Graham, who led a delegation to Egypt and other countries in the region earlier this month, has proposed emergency funding for a "Marshall Plan" to boost Egypt and other countries socially and economically in the region in an effort to counter extremist groups like ISIS.
But there is also growing concern among some on Capitol Hill that the el-Sisi government is exploiting security concerns to quash political dissent.
House Speaker Paul Ryan, who was part of the congressional delegation, said he raised the human rights issue with President al-Sisi.
While Ryan said he was in favor of continuing the military aid, he told el-Sisi that Egypt's human rights record made it "more difficult" to support his government.