The UK leader is visiting allies in the Gulf for talks on how to support the pause in fighting and secure a permanent reopening of the key shipping strait.
A Downing Street spokesperson said: "The Prime Minister spoke to President Trump from Qatar this evening.
"The Prime Minister set out his discussions with Gulf leaders and military planners in the region on the need to restore freedom of navigation in the Strait of Hormuz, as well as the UK's efforts to convene partners to agree a viable plan.
"They agreed that now there is a ceasefire in place and agreement to open the Strait, we are at the next stage of finding a resolution.
"The leaders discussed the need for a practical plan to get shipping moving again as quickly as possible."
Sir Keir earlier said the ships passing through the Strait of Hormuz must have "toll-free navigation" as part of the ceasefire amid reports Iran wants to charge for passage.
Speaking in London, the UK Foreign Secretary also called for toll-free travel through the Strait, warning that trading routes from Qatar, UAE, Bahrain, Kuwait, Iraq, Saudi Arabia and Oman were "all hijacked by Iran so that they can hold the global economy hostage".
Yvette Cooper said: "The fundamental freedoms of the seas must not be unilaterally withdrawn or sold off to individual bidders and nor can there be any place for tolls on an international waterway."
The US president posted on his Truth Social platform: "There are reports that Iran is charging fees to tankers going through the Hormuz Strait — They better not be and, if they are, they better stop now! President DONALD J. TRUMP."
Mr Trump agreed a two-week truce earlier this week with the reopening of the strait a key condition.
But the agreement has come under immediate strain as Israel's bombardment of Beirut prompted Iran to close the shipping lane again amid disagreement over whether Lebanon was included in the ceasefire.
However, Israeli Prime Minister Benjamin Netanyahu said on Thursday he had authorised direct talks with Lebanon "as soon as possible" aimed at disarming Iranian-backed Hezbollah militants and establishing relations between the neighbours.
Sir Keir said Israeli strikes on Lebanon are "wrong" and that it should be included in the ceasefire.
His call with Trump came hours after he was asked about the US President's language in his posts about Iran and said they were "not words I would use".
Trump has repeatedly lashed out publicly at Sir Keir in recent weeks over his failure to initially allow Washington to use UK bases.
Sir Keir reiterated on Thursday that the US is only authorised to use UK bases for "collective self-defence" and said the UK is "monitoring" to make sure that is the case.
