National Investigation Agency (NIA) special judge S. Vijayakumar had Tuesday held the 13 guilty of waging war against the nation but let off five others for lack of evidence.
Of the 13, four were handed out a double life term. They included T. Nazeer, the self-styled south India chief of the terrorist group, Lashkar-e-Taiba.
The case came to light in 2008 when four Kerala youths were shot dead by security forces in Jammu and Kashmir. Nazeer was arrested in 2009 close to the India-Bangladesh border in Meghalaya.
Nazeer is already serving a life sentence for the 2006 Kozhikode twin bomb blasts.