"There'll be a meeting here in the United States sometime in the fall," White House National Security Council spokesman John Kirby said.
The two leaders had agreed to remain in close touch and “to further discuss matters of mutual concern”, Mr Kirby said.
The invitation came as Israel's governing coalition pushes ahead with a contentious plan to overhaul the country's judiciary, despite growing opposition from within the country's military and a wave of mass protests.
The Prime Minister's office said Mr Netanyahu had told Mr Biden that a bill to remove the Supreme Court's ability to strike down government actions it deemed “unreasonable” would be brought for a parliamentary vote next week.
The issue has soured relations between the two allied nations.
“President Biden reiterated in the context of the current debate in Israel about judicial reform, the need for the broadest possible consensus and that shared democratic values have always been and must remain a hallmark of the US-Israel relationship,” Mr Kirby told reporters on Monday.
He added that during the call, the two leaders consulted on co-ordination to counter Iran, including through regular and ongoing joint military exercises.
Mr Kirby said Mr Biden had stressed the need to take measures to maintain the viability of a two-state solution to the Palestinian-Israeli conflict and to improve the security situation and the West Bank.
The US President also expressed concern about continued expansion in the Jewish settlements in the occupied West Bank.
Mr Biden is trying to keep long-time US-Israeli relations on track while facing calls by some American leaders to put pressure on Israel over recent violent incidents in the West Bank. His Democratic Party has become increasingly critical of Israel in recent years.
But no exact date has yet been announced for the meeting and officials on Monday did not specify if the visit would take place at the White House.
“I don't see it as a formal invitation like what [Israeli President Isaac] Herzog is getting or what Netanyahu has got in the past,” Khaled Elgindy, director of Palestine and Palestinian-Israeli Affairs at the Middle East Institute told The National.
On Tuesday, Mr Biden will host Israeli President Isaac Herzog at the White House. Mr Herzog will also address a joint session of the US Congress on Wednesday.
The White House said the meetings with Mr Herzog are expected to focus on Israel's role in the region, Russia's relations with Iran and Tehran's “destabilising behaviour in the region”.
Mr Herzog last visited the White House in October.
“I think the Biden administration wants to register some disapproval with Netanyahu without putting too fine a point on it,” Mr Elgindy said.
“They don't want to bash Netanyahu because that doesn't go over well, domestically.
“It looks like they're doing everything short of a formal Netanyahu visit.”