The two talked on the phone for more than an hour, according to White House press secretary Sarah Huckabee Sanders.
"Had a long and very good conversation with President Putin of Russia," the president wrote in a post on Twitter shortly after Sanders disclosed the call. "As I have always said, long before the Witch Hunt started, getting along with Russia, China, and everyone is a good thing, not a bad thing."
Regarding the investigation by special counsel Robert Mueller, which concluded in March, Sanders said "both leaders knew there was no collusion." The discussion on the matter was brief, she said.
The Kremlin said the call was initiated by "the American side," and did not mention the Mueller probe in its readout of the phone call provided to NBC.
Trump also used the conversation to call on Putin to put pressure on North Korean leader Kim Jong Un to denuclearize, Sanders said. The president has made the denuclearization of the Korean Peninsula a key foreign policy priority.
"....We discussed Trade, Venezuela, Ukraine, North Korea, Nuclear Arms Control and even the 'Russian Hoax.' Very productive talk!" Trump wrote in a followup tweet.
Trump and Putin have spoken on the phone more than half a dozen times since Trump became president, according to official readouts from the White House. Last year, Putin said the two spoke "regularly."
The discussion between the two leaders comes amid tense relations, with a geopolitical standoff in Latin America threatening to break out into greater violence and intense domestic attention on Trump's dealings with Russia.
In recent days, the two countries have warned each other against further intervention in Venezuela, where U.S.-backed opposition leader Juan Guaido is escalating calls for a mass uprising against Nicolas Maduro, who retains Russian support.
"This is our hemisphere," Bolton said Wednesday. "It's not where the Russians ought to be interfering."
Meanwhile, Russian Foreign Minister Sergei Lavrov warned in a phone call to Mike Pompeo, the American secretary of state, that U.S. intervention in the country violated international law and could lead to grave consequences, Reuters reported.
The Trump administration has not ruled out armed intervention. Vice President Mike Pence told CNBC in an interview Friday that "all options" remain on the table, but noted that "we hope for a peaceful transition of power."
The Kremlin said that Putin "stressed that only the Venezuelans themselves have the right to determine the future of their country."
Concerns in Washington also loom over the bilateral relationship. Since Trump was elected, Democrats have accused him of having too cozy a relationship with Putin, criticism that was inflamed for months by the steady drip of news from Mueller's probe.
Attorney General William Barr is facing calls from a number of congressional Democrats to resign over what they say were misleading characterizations of concerns raised by Mueller's prosecutors during his April testimony to Congress ahead of the report's release.
Mueller's investigation into accusations that Trump colluded with Russia during the 2016 campaign dogged much of the first two years of his administration, and "placed a cloud over the Presidency that has only begun to lift in recent weeks," White House lawyer Emmett Flood wrote in a recent letter to Barr that was made public Thursday.
Your moustache must must smell like manure, Walrus Man. Their hemisphere must look like an orange peel. Even if you leave in the countries we have bases on, I’m still pretty sure you’d have to cut around the Ukraine, and Afghanistan, and Vietnam, and Japan, and Korea, and....wait, where is this hemisphere again? Is it vertical???