Sanaa International Airport's general director Khaled al-Shaief said in a post on X the strike had completely destroyed the last of the civilian planes that Yemenia Airways was operating from the airport.
The airport is the largest in Yemen and came back into service last week after temporary repairs and runway restoration following previous Israeli strikes.
It was mainly being used by UN aircraft and the plane destroyed in the latest Israeli strikes. Three other Yemenia Airways planes were destroyed in an attack earlier in May.
"This is a clear message and a direct continuation of the policy we have established: whoever fires at the State of Israel will pay a heavy price," Israel's defence ministry said in a statement.
The Houthis did not immediately respond to a request for comment.
Part of Iran's "Axis of Resistance", a regional alliance that includes Hamas in Gaza and Hezbollah in Lebanon, the Houthis control territory where about 60 per cent of Yemen's population resides.
Since the start of the war in Gaza in October 2023, the group has fired at Israel and at shipping in the Red Sea in what it says are acts of solidarity with the Palestinians.
Most of the dozens of missiles and drones fired towards Israel have been intercepted or fallen short. Israel has carried out a series of retaliatory strikes.
The US also launched intensified strikes against the Houthis this year, before halting the campaign after the Houthis agreed to stop attacks on US ships.
In a statement on Wednesday, Israeli Prime Minister Benjamin Netanyahu said that any harm directed at Israel will be met with greater force.
"But, as I have said more than once, the Houthis are only the symptom. The main driving force behind them is Iran, which is responsible for the aggression emanating from Yemen," Netanyahu said.
