His stopover comes amid political quarreling in Egypt. The Obama administration has been stressing to Morsy and other political figures the importance of political consensus.
Speaking at a meeting with business leaders, Kerry said it is "paramount, essential, urgent that the Egyptian economy get stronger, that it get back on its feet."
Kerry said that there needs to be a sense of security and an agreement with the International Monetary Fund to help jump-start the economy.
Kerry said he spoke with the leaders of Great Britain, France, Germany and Turkey and all want to be helpful "but all of them believe Egypt must make some fundamental economic choices."
Kerry met with Amre Moussa and Nabil El Araby, the former and current heads of the Arab League. He met with opposition leaders on Saturday, but state news said opposition leaders Hamdeen Sabahy and Mohamed Elbaradei decided not to meet with Kerry.
He will meet with representatives of non-governmental organizations and Morsy on Sunday. In his visit with Morsy, he will broach "very specific ways" in which Obama wants to help Egypt, including economic assistance, support for private business, increasing Egyptian exports to the United States and investing in education.
In remarks to reporters on Sunday, he reiterated the importance of economic and political strides.
"There must be a willingness on all sides" in Egypt to make "meaningful compromises," and Egyptians must stay focused on economic and political opportunities to succeed in forging a successful democracy. His visit comes as Egypt has been engulfed in political unrest for months.
He said the United States will help Egyptians achieve their aspirations for democracy and economic opportunity without interference.
"We come here as friends" of Egyptians, not favoring a particular group, person or ideology.
He said "the best way to ensure human rights" in the country is through the "broadest possible" political and economic participation.
Kerry also said he appreciated Morsy's role in helping bring about a cease-fire between Israel and militants in Gaza in fighting there last year.