Mangaraju (31) was found to have hanged himself with a sheet inside the prison toilet.
Jail superintendent Dr Indla Srinivasa Rao said he was mentally unstable and had been treated at the Government Hospital last year for mental illness.
Mangaraju belonged to Petamari-Kukkamarri area under Gumma block in Malkangiri district of neighbouring Odisha, and had joined the Naxals at a young age.
He was arrested near Yebulam village in Vizag Agency area on September 4, 2010. As many as ten cases are pending against him.