Saudi state television identified the locations as Sabuhah village, about 35 km (22 miles) northeast of the Grand Mosque in Mecca, and Wadi al-Maghmas, about 21 km east of the mosque.
The missiles were launched towards the region and intercepted and destroyed, Saudi Arabia's civil defence said in a statement.
The Houthis have repeatedly denied Saudi accusations that they target Mecca and Medina, Islam's two holiest cities, saying their military operations are directed at military and strategic targets elsewhere in Saudi Arabia.
Mecca, home to sites sacred to Muslims worldwide, is the focal point of the annual hajj pilgrimage, one of the five pillars of Islam, which millions of Muslims undertake each year.
"This hostile targeting of civilian objects constitutes a flagrant violation of international humanitarian law and reflects the dangerous hostile approach pursued by the Houthi militia," Saudi Arabia's civil defence said early on Thursday.
The Houthis seized Yemen's capital Sanaa in 2014, prompting Saudi Arabia to intervene militarily the following year in support of the internationally recognised government.
A UN-brokered truce in 2022 largely froze the conflict, but hostilities resumed earlier this year, with the Houthis launching missile and drone attacks on Saudi territory and Riyadh carrying out airstrikes in Yemen.
The latest escalation has threatened the strategic Bab el-Mandeb Strait, a key shipping route linking the Red Sea and the Gulf of Aden.
(Reporting by Hatem Maher; Editing by Chris Reese, Tom Hogue and Kate Mayberry)

A Houthi soldier stands guard in front of a banner depicting the Kaaba, Islam's holiest shrine in Mecca, during a protest against Saudi Arabia, in Sana'a, Yemen, 18 September 2026. Thousands of Houthi supporters demonstrated in Sana'a to reject Saudi military intervention in Yemen amid escalating attacks. The protest comes as Houthi fighters and Saudi-backed Yemeni government forces have been fighting for more than two weeks over control of Yemen's Red Sea coastal areas near the Bab al-Mandab Strait. EPA/YAHYA ARHAB
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