Shinji Aoba, 42, was arrested 10 months after he allegedly set fire to the Kyoto Animation studio, public broadcaster NHK and other media said, citing police.
A police spokesman contacted by AFP declined to comment. A police press conference was expected later Wednesday morning.
Aoba was detained by police shortly after the blaze. He was found with serious burns and taken to hospital. He was reportedly unconscious for weeks.
He is reported to have said "drop dead" before setting alight flammable liquid he poured around the building. Besides the 36 people killed inside, dozens were injured.
A motive for his alleged attack remains unclear, though he reportedly confessed to the arson. Some reports have said Aoba accused Kyoto Animation of plagiarising his work.
Police had held off formally arresting Aoba while he remained in serious condition.
He is still recovering, but police have prepared medical treatment facilities at a police station to which he will be sent, public broadcaster NHK reported.
The horrifying attack on the well-known anime studio was the deadliest violent crime in decades in famously safe Japan and shocked the country.
Many of those killed in the blaze were young, including a 21-year-old woman.
"These are people who carry the Japanese animation industry on their shoulders," Kyoto Animation's president Hideaki Hatta told reporters at the time.
"It's heartbreaking. Japanese jewels were lost."
Kyoto Animation, known by its fans as KyoAni, is well-known both domestically and internationally for its role in producing popular TV anime series including "The Melancholy of Haruhi Suzumiya" and "K-ON!"
While many animation studios are based in Tokyo, the firm 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.