Another 36 people were injured in the attack, some with critical wounds.
Nobody else is believed to be missing, according to a Japanese fire official.
Majority of those caught in the blaze were employees of the popular production studio.
The fire broke out in the three-storey Kyoto Animation building in Japan’s ancient capital, after the suspect sprayed an unidentified liquid to accelerate the flames, police and fire officials said.
Survivors who saw the attacker said he was screaming “You die!” when he dumped the liquid and started the fire, according to Japanese media reports.
Witnesses also claimed he did not work at the production studio.
Hideaki Hatta, head of Kyoto Animation, told reporters the company had recently received threats by emails in the past but responded "sincerely" each time.
Hatta asked,"Why on earth did such violence have to be used?"
On the third floor, more than 10 people were found unresponsive, fire department official Satoshi Fujiwara said.
Some of them were found on the stairs, where they apparently collapsed while gasping for air and trying to go out to the roof, he added.
Six people also found on the first and second floors were presumed dead, Mr Fujiwara said.
Officials said the suspect was also injured and taken to hospital, and police are investigating him on suspicion of arson.
Footage on Japan’s NHK national television showed grey smoke billowing from the charred building. Other footage showed windows blown off.
“There was an explosion, then I heard people shouting, some asking for help,” a woman told TBS TV.
“Black smoke was rising from windows on upper floors, then there was a man struggling to crawl out of the window.”
Kyoto Animation, better known as KyoAni, was founded in 1981 as an animation and comic book production studio, and is known for mega-hit stories featuring high school girls, including Lucky Star, K-On! and Haruhi Suzumiya.
A crowdfunding page called "Help KyoAni Heal" has been up by Texas-based Sentai Filmworks "to help the KyoAni team during this time of need".
As of Thursday afternoon, fans have donated over £328,000 - nearly reaching the £400,000 goal.