Shinji Aoba, 45, is charged with murder, attempted murder and arson after he stormed into Kyoto Animation's No. 1 studio on July 18 2019, and set it on fire.
The blaze killed 36 people and left more than 30 others badly burned or injured.
Aoba appeared before the Kyoto District Court for his trial in a wheelchair and wearing a surgical mask, Japanese media reported.
Prosecutors said he carried out the crime in "revenge", thinking Kyoto Animation had stolen one of his novels which he had submitted for a company contest, but defence lawyers have said he cannot be held criminally responsible.
In a statement, Aoba said the attack was all he could think about at that time but that he never thought so many people would die.
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