The White House said the phone call started at 8:33 am in Washington (1233 GMT). A statement would be issued after the call ended, a spokesman said.
While this was Biden's fifth talk with Xi since becoming president a year and a half ago, it's getting hard to mask deepening mistrust between the two countries.
Already stuck in a trade war, Beijing and Washington increasingly risk open conflict over Taiwan, with little sign of resolution on either front.
"Tensions over China's aggressive, coercive behavior in the Indo-Pacific" will be high on the agenda, said White House National Security Council spokesman John Kirby.
The latest flashpoint is a possible trip by Biden ally and speaker of the House of Representatives, Nancy Pelosi, to the island, which Beijing claims is part of China but has its own distinct, democratic government.
Although US officials frequently visit Taiwan, separated by a narrow strip of water from the Chinese mainland, Beijing considers a Pelosi trip as a major provocation. She's second in line to the US presidency and given her position may travel with military transport.
Washington will "bear the consequences" if the trip, which Pelosi has yet to confirm, goes ahead, China warned Wednesday.
General Mark Milley, chairman of the US joint chiefs of staff, told reporters that if Pelosi asks "for military support, we will do what is necessary to ensure a safe, safe conduct of their business."
And the dispute around Pelosi is the tip of an iceberg, with US officials fearing that Xi is mulling use of force to impose control over democratic Taiwan.
Once considered unlikely, an invasion, or lesser form of military action, is increasingly seen by China watchers as possible -- perhaps even timed to boost Xi's prestige when he moves later this year into a third term.
Biden's contradictory comments on whether the United States would defend Taiwan -- he said in May that it would, before the White House insisted there was no change in the hands-off "strategic ambiguity" policy -- have not helped the tension.