Justice J B Pardiwala issued notice to the government and the authorities of Sabarmati jail on the petition by Prahlad Patel.
Patel said while he was found to have contracted HIV in May 2009, the Mehsana court convicted him in September 2011.
He had written to the state's Home Department in 2014 seeking pardon and release on health ground, but got no response, he said.
He also alleged that he was not getting proper treatment in the jail.
More From This Section
The next hearing is scheduled for June 21.
As many as 32 persons were killed in Sardarpura during the post-Godhra violence in Gujarat in 2002.
Patel and 30 others were awarded life sentence. The high court had upheld the conviction of 17 of them last year.