An Israeli military statement said that navy ships "struck terror targets belonging to the Huthi terrorist regime" in Hodeida, on Yemen's Red Sea coast, "to stop the use of the port for military purposes".
It said the port was "used to transfer weapons".
Israel has carried out numerous attacks on Huthi-controlled areas of Yemen, including on ports and the airport in the capital Sanaa, since the rebel group began launching missiles and drones after the start of the Gaza war in October 2023.
The Iran-backed Huthis, who say they are acting in solidarity with Palestinians, paused their attacks during a two-month Gaza ceasefire that ended in March, but renewed them after Israel resumed its military campaign in the Palestinian territory.
Late Tuesday, the Israeli military said it had "identified the launch of a missile from Yemen toward Israeli territory", adding that sirens were sounded in several areas.
AFP reporters heard loud booms over Jerusalem, similar to past interceptions.
The Huthis claimed responsibility for the launch, with the group's military spokesman Yahya Saree saying in a video statement that fighters had fired "two ballistic missiles" at Israel's main airport.
In Hodeida earlier, the Huthis' Al-Masirah TV channel said "two strikes by the Israeli enemy targeted the docks of the port".
In a post on X, Israeli Defence Minister Israel Katz said: "We warned the Huthi terror organisation that if they continued firing toward Israel, they would face a powerful response and be subjected to a naval and aerial blockade."
Military spokesman Avichay Adraee had warned civilians to evacuate three Huthi-held ports including Hodeida "for their own security", in a post on X and Telegram.
Israeli air defences have intercepted most of the projectiles fired by the Yemeni rebels throughout the Gaza war, which broke out with the October 7, 2023 attack by Huthi-allied Palestinian group Hamas.
One missile fired in early May hit inside the perimeter of Ben Gurion airport, Israel's main international gateway, gouging a hole near the terminal building and wounding several people.
Last month, Israeli air strikes blew up the last remaining plane at the Sanaa airport, weeks after an earlier attack inflicted major damage.
Israel has also threatened to target the Huthi leadership.
The Yemeni rebels have been at war with a Saudi-led coalition since 2015 in a conflict that killed hundreds of thousands of people and triggered a major humanitarian crisis in Yemen, although fighting has decreased significantly since a UN-negotiated truce in 2022.
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