The two leaders held the conversation on Thursday, according to the Kremlin, which said the discussions centered on the years-long conflict in eastern Ukraine, Presstv Reported.
They also discussed the return of prisoners. Zelenskiy said he would try to free Ukrainians imprisoned in Russia. These include 24 Ukrainian sailors, among others.
Moscow and Kiev agreed that such consultations would continue at expert level, the Kremlin said in a statement.
A conflict has erupted between the two countries since 2014, when the Black Sea peninsula of Crimea rejoined Russia following a referendum with more than 90 percent of participants voting in favor of the move.
The West brands the reunification as annexation of Ukrainian land by Russia.
In siding with Ukraine, the EU, and some other Western countries have followed Washington's lead in leveling several rounds of sanctions against the Moscow.
On Monday, Zelenskiy proposed holding talks with Putin to discuss the conflict in a meeting in Minsk, Belarus.
“I suggest the following line-up for talks: me, you, US President Donald Trump, British Prime Minister Theresa May, German Chancellor Angela Merkel [and] French President Emmanuel Macron," Zelensky said in a social media video address.
"Let's discuss who Crimea belongs to and who isn't in the Donbass region," he said.
In response to the proposal, Putin said earlier on Thursday that Moscow is ready for "any kind of talks" on the Ukrainian issue.
Belarus — a close ally of Russia — also said that it would be ready to host a new round of talks between Kiev and Moscow.
Belarusian President Alexander Lukashenko "absolutely supports the proposal by Volodymyr Zelensky,” his office said in a statement.
"You cannot look at each other through gun sights. You need to sit down and solve the problems that have accumulated," it added.
The statement also said that the conflict must be solved by the three countries of Ukraine, Russia and Belarus.
Back in 2015, peace talks in Minsk resulted in the Minsk II ceasefire agreement.
Since then, the both parties have on numerous occasions accused each other of violating the ceasefire.
Putin’s spokesman said, “This is an absolutely new format.”
“This is a new initiative. Certainly it will be considered, but I cannot give any response now," Peskov said.
Russia-Georgia tensions on the rise
In the meantime, new tensions have been mounting between Russia and its neighbor Georgia.
Angry protests broke out in the capital Tbilisi over a visit by a Russian lawmaker, and the continued presence of Russian troops on Georgian soil.
Moscow responded with a ban on direct flights, with lawmakers unanimously backing a resolution on Tuesday calling for sanctions to be imposed on Georgia.
European Council President Donald Tusk reacted to the flight ban, calling the move as “unjustified and disproportional.”
Tusk said that “the EU stands with Georgia in solidarity and with a full commitment to your sovereignty and territorial integrity.”
Georgia— an ally of the United States —fought and lost a war against Russia in 2008. Ever since, the two countries have not had diplomatic ties.