The attack, which the US president said was "not necessary" and "very bad timing" as he pushes for peace, also wounded 90 people, smashed buildings and set off fires, Ukrainian officials said.
Rescuers were still recovering bodies from the rubble more than 12 hours later.
The attack comes at a critical moment in Russia's war in Ukraine, which began with the Kremlin's full-scale invasion in 2022.
Both Ukraine and Russia are trying to show Trump they are making progress towards his goal of a rapid peace deal.
"I am not happy with the Russian strikes on KYIV. Not necessary, and very bad timing. Vladimir, STOP! 5000 soldiers a week are dying. Lets get the Peace Deal DONE!" Trump said on Truth Social, referring to the Russian president.
The White House has threatened to abandon its efforts if no progress is made soon.
Trump upbraided Zelenskiy on Wednesday over a comment in which the Ukrainian president repeated that his government would not recognise Russia's occupation of Crimea.
Trump has used a markedly more gentle tone in his statements about Putin than with Zelenskiy, whom he at one point referred to as a "dictator".
Zelenskiy's five-year term was supposed to end in 2024 but presidential and parliamentary elections cannot be held under martial law, which Ukraine imposed in February 2022.
Trump's special envoy is expected to meet Putin on Friday for more talks, a US official has said.
Zelenskiy said on Thursday he believed that a document with proposals that emerged from Wednesday's talks between officials from Ukraine and European allies in London was now on Trump's table.
"...I believe that today, this format, this document, is on President Trump's desk," Zelenskiy told a press conference in South Africa.
"Anything that contradicts our values or our constitution cannot be included in any agreement."
Zelenskiy, who cut short a trip to South Africa on Thursday after the Russian strike, said he did not see signs the US was putting strong pressure on Russia.
The Russian defence ministry said it carried out what it described as a massive overnight strike against Ukraine's military-industrial complex using air, land and sea-based long-range high-precision weapons and drones.
Rescue teams were operating at 13 sites in Kyiv with climbing specialists and sniffer dogs, the emergency services said.
Forty fires had broken out.
"Mobile telephones are heard ringing beneath rubble. The search will continue until it becomes clear that they have got everyone," it said.
Updating an earlier death toll, Tymur Tkachenko, the head of the Kyiv city military administration, said: "Rescuers have retrieved two more bodies from under the rubble in the Sviatoshynskyi district. We now have 12 dead."
Fires had broken out in garages, administrative buildings and falling metal fragments had struck vehicles.
"There was the air raid siren, we did not even have time to dress to go out of the apartment. One blast came after the other, all windows were blown out, doors, walls, my husband and son were thrown to the other side," Kyiv resident Viktoria Bakal said.
A Ukrainian military source told Reuters the missile that struck a residential building in the Sviatoshynskyi district west of Kyiv's centre was a North Korean KN-23 (KN-23A) ballistic missile.
Ukrainian Foreign Minister Andrii Sybiha said on X that the "brutal strikes" showed that Russia, not Ukraine, was the obstacle to peace.
Russia launched 145 drones and 70 missiles, including 11 ballistic missiles, in the overnight attack, Ukraine's air force said on Telegram, adding that air force units shot down 112 targets.
Interior Minister Ihor Klymenko said that apart from Kyiv and the surrounding region, seven other regions were under "mass" attack.
Damage was reported in the northeastern city of Kharkiv, Ukraine's second biggest, in the Zhytomyr region west of Kyiv and in the industrial city of Pavlohrad, which lies in the central Dnipropetrovsk region.
