The USS Mason and amphibious transport dock USS Ponce were operating north of the Bab al-Mandab Strait, between the southwest coast of Yemen and Djibouti. Defensive salvos were fired, and neither ship was damaged.
This is the second such incident in four days. Missiles were fired at the Mason on Sunday in the same area.
"We are going to find out who did it and take action accordingly," said Capt. Jeff Davis, a US Defense Department spokesman said, according to NBC, referring to Sunday's incident. "Anybody who puts US Navy ships at risk does so at their own peril."
On Monday, an anonymous Houthi official speaking to Reuters denied targeting any ship off Yemeni waters. Meanwhile, Saudi Arabia, the US, and the Riyadh-backed Hadi government have regularly accused iran of supplying weapons to the Houthis, a charge that Tehran has vehemently denied.
The first attack came on the same day that US Secretary of State John Kerry expressed Washington's "deep concern" over a Saudi airstrike on a funeral procession in Houthi-controlled Sanaa that claimed the lives of at least 213 people and left hundreds more injured. Saudi Arabia denied involvement in the incident and expressed readiness to cooperate with the US in investigating the attack.