Many more people were feared to have been killed after the two strikes that hit the depot in the Fajj Attan area of Sanaa, which was covered in thick black clouds of smoke.
Medics at four hospitals in the capital said at least 18 civilians were killed and some 300 others wounded.
The hilltop base belongs to the missile brigade of the elite Republican Guard, which remained loyal to former president Ali Abdullah Saleh who has been accused of siding with the Huthi rebels in their fight against the government.
The Shiite rebels have seized control of large parts of the Arabian Peninsula nation, including Sanaa, and fought fierce battles with pro-government forces.
A coalition of Sunni Arab nations led by Saudi Arabia launched the air campaign against the rebels last month, vowing to restore the authority of President Abedrabbo Mansour Hadi, who fled to Riyadh as the militiamen advanced on his southern stronghold of Aden.
Riyadh has accused Iran, the main Shiite power, of backing the rebels and fears a Tehran-friendly regime taking control of the country on its southern border.
The United Nations says the fighting and air strikes have left hundreds dead and thousands wounded, and there has been increasing concern of a huge humanitarian crisis.
Calls have been growing for peace talks to end the conflict, but authorities on Monday rejected an Iranian offer to mediate talks.
"Any mediation effort coming from Iran is unacceptable because Iran is involved in the Yemen issue," Yemeni Foreign Minister Riyadh Yassin said on the sidelines of an economic meeting in Kuwait City.
"After that we can talk about dialogue and a political solution. But now there is no room for negotiations.
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