Gandhinagar Akshardham temple attack accused Yasin Butt was arrested by the Gujarat Anti-Terrorism Squad (ATS) from Anantnag district of Jammu and Kashmir on Friday.
He was later taken to Ahmedabad.
The attack was carried out by two terrorists with alleged links to Lashkar-e-Taiba (LeT) on September 24, 2002.
The two terrorists were eliminated by the National Security Guard (NSG) commandos.
At least 32 people were killed and over 80 others injured in the attack.
In May 2014, the Supreme Court had discharged all six convicts, who were arrested earlier in the case.
One more person was arrested in November last year.