The new attack comes with the NATO summit under way in Ankara, where US President Donald Trump is due to hold talks with Ukrainian President Volodymyr Zelenskiy.
While Ukraine's air defences intercepted 139 of the 169 drones during the overnight strikes on the country, they were again unable to down any of the five ballistic missiles used by Russia, air force data showed.
Moscow has stepped up its air war on Ukraine in recent months as its ground advances have largely stalled and Ukrainian attacks on its military logistics and oil industry triggered widespread fuel shortages.
In July alone, Russian strikes at the Ukrainian capital and surrounding region have killed 60 people.
Since the start of July, air defences shot down just four out of 54 ballistic missiles fired by Russia, according to air force data.
Explosions ripped through Kyiv just before the air raid siren sounded, Reuters witnesses reported.
A woman was killed and two people were wounded in the overnight attack on Kyiv, authorities said.
Kyiv mayor Vitali Klitschko said the strikes had caused fires in a storage area and a non-residential building in two districts on either side of the Dnipro River.
Reuters footage showed two warehouses in flames after the strikes, with firefighters battling the fires from crane ladder platforms into the morning.
Kharkiv, Ukraine's second-biggest city, also came under missile attack overnight, local officials said, reporting damage to private homes and a church.
Another missile strike on Wednesday on a residential building killed two, Mayor Ihor Terekhov said.
Zelenskiy has repeatedly pleaded for US-made interceptors - the only weapon in Ukraine's arsenal that can shoot down ballistic projectiles, whose high velocity and steep flight path make them difficult to stop.
He is expected to raise the issue with Trump during their meeting at the summit on Wednesday.
Trump, who had spoken with both Zelenskiy and Russian President Vladimir Putin before the summit, said on Tuesday in Ankara he believed the war could be "settled, hopefully soon".
Putin has said he will press ahead with his war despite the mounting difficulties for Russia.
Moscow has demanded that Kyiv cede the rest of its eastern Donetsk region that it has been unable to conquer in more than four years of fighting.
In Russia, Ukraine's overnight drone attacks killed one person and damaged numerous industrial sites, local authorities said.
