The raids on the army headquarters in central Sanaa came a day after the kingdom's air defences shot down a Scud missile fired from the war-torn country.
They also followed the UN confirmation of June 14 as the start date for peace talks between warring Yemen factions in Geneva, which both the country's Huthi rebels and its exiled government said they will attend.
"At least 20 civilians and 25 soldiers and officers were killed" in four raids that hit the headquarters in the Tahrir residential neighbourhood in central Sanaa, the medic said.
The raids hit residential buildings, including five houses that were completely destroyed, witnesses said.
Read: Saudi Arabia says shoots down Scud missile fired by Yemeni forces
The rebel-controlled Saba news agency said 44 people were killed and more than 100 wounded "including woman and children".
Seven Sunday air raids targeted the Jumaineh military base, east of the capital Sanaa, according to witnesses.
The base belongs to the elite Republican Guard that has remained loyal to former president Ali Abdullah Saleh, who has allied himself with the Huthis.
Other raids hit an arms depot at the Nahdain hill, also south of Sanaa.
At least four pre-dawn air raids targeted the rebel-held headquarters of the armed forces in the centre of the capital, triggering explosions that damaged nearby buildings and forced residents to flee, an AFP photographer reported.
Several rebel positions in the north, mainly in the Huthi stronghold Saada province and the provinces of Hajja and Amran, were heavily bombarded overnight by the coalition, witnesses said.
In the south, coalition jets targeted rebel positions on the northern and western outskirts of second city Aden in support of southern fighters backing exiled President Abedrabbo Mansour Hadi.
Fighters from the southern Popular Resistance were attempting to prevent rebels from advancing towards the neighbourhoods of Al-Masnoura, Dar Saad, Sheikh Othman and Al-Buraiqa, according to a pro-Hadi military commander.
Read: Regional crisis: ‘Negotiations with Houthis only way out’
"Several Huthi rebels and allies were killed or wounded," said General Fadhl Baesh.
Riyadh said the Huthis fired a Scud missile at Saudi territory Saturday, a day after their rebel allies killed four Saudi soldiers in cross-border attacks.
Yemen has been engulfed in turmoil since the Iranian-backed Huthis seized the capital in September and advanced on the southern city of Aden, forcing Hadi to flee into exile in Saudi Arabia.
The Saudi-led coalition has carried out air strikes on Yemen since March 26 to push back the Huthis and restore Hadi's authority. More than 2,000 people have died since the air campaign began.
The United Nations urged Yemeni parties to engage in talks in Geneva without preconditions.
Read: Four things that Saudi airstrikes in Yemen put into perspective
The meeting would be the first significant effort to stop the fighting, which has led to what the UN says is a catastrophic humanitarian situation.
Huthi rebels said they will attend the talks, and Yemen's government exiled in Riyadh also said it would take part.
In line with UN Security Council Resolution 2216, Hadi's government had refused to attend unless the rebels pulled back from at least some of the territory they have seized.
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