Ahmed al-Rahawi was killed in a Thursday strike in Sanaa along with several ministers, the rebels said in a statement.
Other ministers and officials were wounded, the statement added without providing further details.
The leader was targeted along with other members of his Houthi-controlled government during a "routine workshop held by the government to evaluate its activities and performance over the past year," the Houthi statement said.
Thursday's Israeli strike occurred as the rebel-owned television station was broadcasting a speech for Abdul Malik al-Houthi, the secretive leader of the rebel group, where he was sharing updates on the latest Gaza developments and vowing retaliation against Israel.
Senior Houthi officials used to gather to watch al-Houthi's pre-recorded speeches.
On Thursday, the Israeli military said that it "precisely struck a Houthi terrorist regime military target in the area of Sanaa in Yemen."
The military had no immediate comment on Saturday's announcement of the prime minister's killing.
The prime minister hailed from the southern province of Abyan and was an ally to former Yemeni President Ali Abdullah Saleh.
He allied himself with the Houthis when the rebels overran Sanaa and much of the north and centre of the country in 2014, initiating the country's long-running civil war.
He was appointed as prime minister in August 2024.
Al-Rahawi is the most senior Houthi official to be killed since the United States and Israel began their air and naval campaign in response to the rebels' missile and drone attacks on Israel and on ships in the Red Sea.
The Houthis launched a campaign targeting ships in response to the Israel-Hamas war in the Gaza Strip, saying they were doing so in solidarity with the Palestinians.
Their attacks over the past two years have upended shipping in the Red Sea, through which about $US1 ($A1.5) trillion of goods passes each year.
In May, the Trump administration announced a deal with the Houthis to end the air strikes in return for an end to attacks on shipping.
The rebels, however, said the agreement did not include halting attacks on targets it believed were aligned with Israel.
