Kremlin spokesman Dmitry Peskov confirmed the call, saying it would take place Thursday evening Russian time.
Russia has sent tens of thousands of troops to the border with Ukraine, according to Western officials who fear a repeat of 2014 when Moscow seized the Crimean peninsula and a pro-Russia insurgency broke out in eastern Ukraine that has left more than 13,000 people dead.
In a potential step to defuse tensions, senior US and Russian officials plan to meet on January 10 in Geneva.
The meeting comes after Russia offered proposals to the United States that included calls not to expand NATO eastward or to set up bases in former Soviet republics.
The United States has called some of the Russian positions non-starters but said it is willing to talk and will also bring up its own concerns.
The dialogue was set up when Putin and Biden met in Geneva in June. US officials at the time sought at least for greater predictability in the tense relationship with Russia -- hopes that have been dashed with the latest troop movements.
The administration official made clear there were no plans for another in-person summit.
Russian foreign minister Sergei Lavrov has vowed that Moscow will take a "hard line" in the Geneva talks in defending its interests.
Ahead of the US-Russia talks, US Secretary of State Antony Blinken spoke by telephone on Wednesday with Ukrainian President Volodymyr Zelensky.
"I was assured of full US support for Ukraine in countering Russian aggression," Zelensky tweeted afterward.
Blinken also spoke separately to his counterparts from Britain, France and Germany on "coordination to deter any further Russian aggression against Ukraine," state department spokesman Ned Price said.
The Western foreign ministers "affirmed the consensus among allies and partners to impose massive consequences and severe costs on Russia for such actions," Price said.
The Biden administration has vowed to take all actions in lockstep with its European allies. Following the Geneva talks, Russian delegates will meet with delegates of the NATO alliance ahead of a meeting of the Organization for Security and Co-operation in Europe, a key Cold War forum that brings together Moscow and the West.
Russia has already been under sanctions since its 2014 actions in Ukraine, which came in response to the toppling of a government in Kiev that had resisted calls to move closer to the West.
Biden has not spelled out what new measures could be in place, but reports say the United States could move to disconnect Russia from the SWIFT system that connects the world's banks, a major blow for a leading economy.
Fearful of Russia, Ukraine and former Soviet republic Georgia have sought to join NATO, although European members have made clear that they are not enthusiastic about their accession.