The military on Saturday said sirens were activated in a number of areas in Israel after the missile was launched.
US President Donald Trump in March ordered large-scale strikes against the Houthis to reduce their capabilities and deter them from attacking ships in the Red Sea.
The deadly strikes on the group were the biggest US military operation in the Middle East since Trump took office in January.
The Houthis say their attacks on Israel and Red Sea shipping are in solidarity with the Palestinians over the war between Hamas and Israel in Gaza.
The group pledged to expand its range of targets in Israel in retaliation for a renewed offensive in Gaza that began two months ago.
The Yemeni group have also vowed to continue attacks on shipping after the US launched its biggest and deadliest military operation in Yemen since Trump took office.
Meanwhile, a ship bound for Gaza carrying humanitarian aid and activists has been bombed by drones in international waters off Malta, its organisers say, alleging Israel was to blame.
The Israeli foreign ministry did not respond to a request for comment on the allegation by the Freedom Flotilla Coalition, an international non-governmental group.
The Maltese government said the vessel and its crew were secured in the early hours of Friday morning after a nearby tug assisted with firefighting operations
Turkey's foreign ministry said Turkish nationals were on board at the time of the incident and it was working with Maltese authorities to transfer them to a safe location.
A ceasefire between Israel and Hamas broke down in March, with both sides blaming each other, and Israel sent troops back into Gaza and resumed airstrikes.
The NGO published video footage, filmed in darkness, showing a fire on one of its ships, the Conscience. The footage showed lights in the sky in front of the ship and the sound of explosions could be heard.
The Maltese government said maritime authorities had received a mayday call shortly after midnight local time from a vessel outside of territorial waters, with 12 crew members and four civilians on board, reporting a fire.
It said a nearby tug headed to the scene and launched firefighting operations and a Maltese patrol vessel was dispatched. After several hours, the vessel and its crew were secure, it said, adding that crew had refused to board the tug.
The Gaza war started after Hamas-led fighters killed 1200 people and took 251 hostages to Gaza in the October 7, 2023 attacks, according to Israeli tallies. Since then, Israel's offensive on the enclave killed more than 52,000, according to Palestinian health officials.
Since March 2, Israel has completely cut off all supplies to the 2.3 million residents of the enclave, and food stockpiled during a ceasefire at the start of the year has all but run out, according to international aid agencies.
Israel accuses the Hamas militants who have run Gaza of exploiting aid - which Hamas denies - and says it must keep all supplies out to prevent the fighters from getting it.
Another coalition ship on a similar mission to Gaza in 2010 was stopped and boarded by Israeli troops, and nine activists died. Other ships have similarly been stopped and boarded, without loss of life.
Hamas issued a statement about the incident off Malta, accusing Israel of "piracy" and "state terrorism".
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