"Following the sirens that sounded recently in several areas in Israel, a missile that was launched from Yemen was intercepted" before "crossing into Israeli territory", a military statement said.
The Huthis announced a "military operation" targeting the Nevatim air base in southern Israel, claiming that "the missile reached its target".
In a separate incident, the Israeli military said a drone "that was on its way to Israeli territory from the east was intercepted" by the air force.
Huthi military spokesman Yahya Saree later said the rebels fired two drones at Israel and more at the US navy's Harry S Truman aircraft carrier battle group.
Yemen, large parts of which are under the control of the Iran-backed Huthis, is located to Israel's southeast.
Other countries to Israel's east include Iraq, where Tehran-aligned militants have claimed a number of attacks targeting Israel since the Gaza war began.
The Huthi rebels have repeatedly launched missiles and drones at Israel since the war in Gaza broke out in October 2023 in what they say is a show of solidarity with the Palestinians.
The Huthis have also targeted ships they accuse of having ties to Israel as they travel on the Red Sea -- a vital waterway for global trade.
They had temporarily paused their attacks during a recent two-month ceasefire in Gaza.
According to Israel's army radio, the missile intercepted overnight was the 22nd fired by the Huthis since they resumed their attacks after Israel renewed its Gaza offensive on March 18.
Since March 15, Israel's key ally the United States has stepped up its attacks on the Huthis, targeting rebel positions in Yemen with near-daily air strikes.