Ashish Pandey, one of the five absconding accused in the case, was arrested from Aslali locality by Crime Branch sleuths, a police official said.
A mob had attacked Gulberg Society, a pre-dominantly Muslim colony in Ahmedabad, on February 28, 2002, killing 69 persons including former Congress MP Ehsan Jafri. It was one of the worst incidents of violence during the post-Godhra riots.
"Pandey was absconding ever since he was named as an accused in the FIR lodged in 2002 after the incident. He lived in Naroda locality with his family, but had fled to evade arrest and thereafter lived in different cities including Haridwar and Vapi and worked in the transport business," said the official.
Police had got a tip-off that Pandey was in the city in connection with his work, he said.
He was handed over to the Special Investigation Team (SIT) which probed the case. He will be produced before a court tomorrow.
A special court for SIT cases had, in June 2016, convicted 24 persons in the Gulberg case, awarding life imprisonment to 11 of them. Thirty-six others were acquitted. With the arrest of Pandey, four more accused are still at large.