Kasam Ibrahim Bhamedi, a resident of Ragadia in Godhra, was apprehended from Dahod railway station, about 200km from here, ATS officials said.
The 53-year-old is the third absconding accused to be arrested in less than a fortnight for the horrific incident in Godhra, about 125km from here, where Sabarmati Express was set afire on February 27, 2002, by a mob killing 59 passengers.
The ghastly train attack had triggered widespread riots in Gujarat in which over 1,000 people were killed.
Recently, officials learnt that Bhamedi is in Madhya Pradesh, where he went with a religious group.
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"We have been tracking his movements since the last one month and we learnt that he will enter Gujarat from Madhya Pradesh by train. Based on that tip-off, we kept a watch at Dahod station today and nabbed him as soon as he arrived," said ATS Inspector B M Karatiya.
According to ATS, Bhamedi was part of a mob which pelted stones at and broke window panes of the S6 coach of Sabarmati Express before it was set ablaze.
He is the third wanted accused in the train carnage case to be nabbed by Gujarat Police this month. On July 16, Local Crime Branch (LCB) officials of Godhra had nabbed Kadir Abdul Gani from the town.
On July 23, Godhra LCB rounded up another wanted accused Hussain Suleman Mohan from Jhabua in Madhya Pradsh.