Acting on a tip-off, the cadre, identified as Konan Sangma of Chengpara village was apprehended from Purakhasi market at around 1:30 PM, they said.
BSF seized a 7.65 mm USA-made pistol, two magazines and 9 RDS from his possession.
Preliminary investigation revealed that Konan had joined the group last year. He received training in the jungles of East Garo Hills district, BSF officials said.
The Centre had declared the GNLA an outlawed organisation in January for criminal activities like intimidation, kidnapping, extorting and killing of civilians and security personnel.