The HMS Diamond warship used a Sea Viper missile system to shoot down the missile on Wednesday, the ministry said.
"The UK continues to be at the forefront of the international response to the Iranian-backed Huthis' dangerous attacks on commercial vessels, which have claimed the lives of international mariners," Defence Secretary Grant Shapps said.
"I want to thank the brave crew of HMS Diamond for her vital role in saving innocent lives and protecting international shipping from illegal Houthi attacks."
US and British forces on January 12 fired their first joint strikes aimed at reducing the Huthis' ability to target vessels transiting the key Red Sea trade route. The Huthis says the attacks are in support of Palestinians in the Gaza Strip, where Israel is at war with Hamas.
The Huthis began targeting Red Sea shipping in November.
The US military has also carried out unilateral air raids, but the Huthis have vowed to continue their attacks.
The Red Sea carries about 12 percent of international maritime traffic. Since the attacks started, several shipping firms have stopped using the waterway, instead taking the longer and more expensive route around the Cape of Good Hope in South Africa.
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