Shinji Aoba is in police custody in hospital and is being treated for burns before he can be questioned.
The fire swept through Kyoto Animation (KyoAni) on Thursday, claiming at least 33 lives and injuring many people in one of Japan's mass killings in years.
People who witnessed Shinji Aoba's arrest said they heard him complaining that the company had stolen his ideas.
In the wake of the attack, dozens of people have gathered outside the premises of the studio, laying flowers and offering prayers.
A crowdfunding campaign has also raised more than $1.3m (£1.04m) to assist victims and their families.
KyoAni produces films and graphic novels, and is well regarded by fans for the quality of its productions.
Police detained Shinji Aoba on suspicion of setting fire to the building.
The BBC's Tokyo Correspondent Rupert Wingfield-Hayes says CCTV footage from a nearby petrol station appears to show him filling up two containers with petrol shortly before the incident.
The suspect's relationship with the company is still unclear, along with his potential motive. People who witnessed the suspect's arrest said he was visibly angry and could be heard complaining that he had been plagiarised.
Kyoto Animation's president has said he recently received threatening letters, but has no idea if they were connected to the attack.