The comments came as a key lawmaker said he wouldn't allow the release of any US aid to Egypt until the government proves it is committed to the rule of law.
Meeting with Egyptian Foreign Minister Nabil Fahmy at the state department, Kerry said the US wants Egypt to succeed as a democracy and called its new constitution a positive step.
But, as Egypt prepares for elections next month, he described the mass death sentences handed down to supporters of the country's deposed president as troubling and calling into question the rule of law.
"There have been disturbing decisions within the judicial process, the court system that have raised serious challenges for all of us," Kerry said.
"We really are looking for certain things to happen that will give people the sense of confidence about this road ahead," he said. "It's actions, not words, that will make the difference."
Egypt is struggling to restore representative government following last year's military ouster of its president, Mohammed Morsi, who won a democratic election after protesters toppled long-time autocrat Hosni Mubarak. The country has been plagued by unrest and militant attacks since Morsi's July overthrow.
Egypt's military-backed interim government has launched a sweeping campaign against Morsi's backers and members of his Muslim Brotherhood, killing hundreds and jailing thousands.
Kerry and Fahmy met a day after an Egyptian judge sentenced more than 680 people to death stemming from last year's post-coup violence in a mass trial that was widely denounced in the West and by human rights groups.
Fahmy acknowledged Egypt faces "challenges" but said he was confident they would be overcome. He said the recent verdicts were rendered by an independent judiciary.
"We need to deal with the challenges we face without disturbing institutional relationships," he said, referring to the courts.
"They are completely independent from the government, but, of course, they are part of what Egypt is all about," Fahmy said. "I can't comment on the content of the decisions themselves (but) I am confident that due process is allowed and that the legal system will ultimately end up with proper decisions in each of these cases."
He added: "We will build a democracy based on the rule of law."
The verdict came less than a week after Kerry certified to Congress that Egypt is upholding its peace treaty with Israel and strategic commitments to the US, freeing up hundreds of millions of dollars in assistance. The Pentagon released a hold on the delivery of 10 Apache helicopters to Egypt to help its military combat extremists.
Kerry has not yet certified that Egypt is meeting the democratic standards required for the remainder of the $1.5bn in US assistance to be sent. But even the $680m he has approved is in jeopardy after Senator Patrick Leahy, a Democrat, raised objections on the Senate floor on Tuesday.
"I am not prepared to sign off on the delivery of additional aid for the Egyptian military until we have a better understanding of how the aid would be used, and we see convincing evidence that the government is committed to the rule of law," said Leahy, who chairs the Senate Appropriations panel for US foreign operations.
Hours after his Senate speech, Leahy lashed into Egypt's government again.
"No country with any sense of morality, with any sense of human values, with any sense of honesty ... is going to sentence hundreds of people to death after 40- or 50-minute trials," he told reporters. "It's obscene. It's wrong. And the United States should not be supporting a country like that."
Senator John McCain said he was working on a Egypt bill with Republican colleague Senator Lindsey Graham. Their legislation, however, would only affect economic aid to Egypt's government.
"We're not going to be able to stop the military aid, No. 1," McCain said. "No. 2, they are reasserting security in the Sinai. That's in our interests."