One suspect is in custody but the motive for the apparent attack remains unclear. Here is what we know:
HOW DID THE FIRE BREAK OUT?
Local fire stations began receiving emergency calls around 10.30am (9.30am Singapore time) on Thursday morning (Jul 18), with people describing the sound of explosions at a building belonging to the Kyoto Animation production firm.
Police said a man was believed to have doused the building with a flammable substance that he set alight.
The blaze quickly engulfed the three-storey building, trapping dozens of people inside.
Eyewitnesses said the blaze was so fierce that they were unable to even approach the building as desperate people jumped from the windows to escape.
It took firefighters hours to bring the blaze under control.
The flames gutted the building, which fire department officials said was up to date with fire safety rules.
WHO ARE THE VICTIMS?
Most of 33 people killed are believed to be employees of Kyoto Animation, an animation production studio based in Uji city.
Kyoto prefectural police said victims included 12 men, 20 women, and one person who has not yet been identified.
Many of the company's employees were believed to be young, among them 21-year-old Megumi Ono, whose status was unclear on Friday morning.
Her grandfather Kazuo Okada told public broadcaster NHK he was still searching for her.
"It turns out that (she) was on the second floor ... her name was not on the list of people sent to hospitals," he said.
"I want to see her face," he said as he broke down with emotion.
WHO IS THE SUSPECT?
A man, identified on Friday as 41-year-old Shinji Aoba, has been detained by police.
Local media said his driving licence shows that he lives in Saitama, an area north of Tokyo.
He is reported to have screamed "Die!" before setting light to flammable liquid he poured around the building.
But his motive for the apparent attack remains unclear, though he reportedly confessed the arson after his detention.
He suffered serious burns in the fire and was taken to hospital after being detained. He was reportedly unconscious on Friday.
The man appears to have no links to Kyoto Animation, but there were reports he had accused the firm of plagiarism.
The local Kyoto Shimbun reported he told police: "I set the fire because they stole novels."
WHAT IS KYOTO ANIMATION?
Kyoto Animation is a firm well-known among anime fans for its role in producing popular TV anime series including The Melancholy Of Haruhi Suzumiya and K-On!
Founded in 1981, it had 154 employees and some of its dozens of animations became popular enough to have movie theatre versions released.
While many animation studios are based in Tokyo, the firm - known by fans as KyoAni - reportedly felt strongly about remaining in the ancient Japanese city of Kyoto.
Its work often featured elaborate screenshots described as "KyoAni quality" by enthusiastic fans.
Anime fans at home and abroad tweeted their support with the hashtag #KyoAniStrong and #PrayForKyoAni.
"These are people who carry the Japanese animation industry on their shoulders," Kyoto Animation's president Hideaki Hatta told reporters.
"It's heartbreaking. Japanese jewels were lost," he said.
HAVE THERE BEEN SIMILAR ATTACKS?
Violent crime and particularly mass casualty incidents are vanishingly rare in Japan, which has strict gun control laws.
But there have been past instances of arson, including a 2008 attack on a video shop in Osaka that killed 16 people.
Arson is considered a particularly serious offence in Japan, where many buildings are made of wood and extremely fire-prone. The Osaka attacker is on death row.
In 2001, a devastating fire in Tokyo's Kabukicho entertainment district killed 44 people. Police investigated the blaze as an arson attack but never charged anyone for deliberately starting the fire.
More recently, there have been mass stabbing attacks, including a 2016 rampage by a knife-wielding man at a care centre for the disabled in suburban Tokyo that killed 19 people.