BSF sources said the arrest occurred late Sunday, after the Pakistani, identified as Muhammad Imran Khan of Sahiwal district, was found to have stayed in the home of a man in Hariya Chak village of Kathua district for more than two years.
He was arrested as he was attempting to return to Pakistan.
The man who offered the Pakistan national shelter has also been arrested by police on suspicion of complicity in militancy-related activities.
The arrests have occurred in the same village, Hariya Chak, where three Pakistani militants who attacked the Hira Nagar police station in Kathua district and later an army camp in Samba Sep 26 this year were first spotted.
Ten people including eight security men and two civilians were killed in the Sep 26 attack in Jammu region.
The three militants were later killed by security forces.
The arrest comes as major embarrassment for security forces.
Hariya Chak village had been thoroughly searched after Sep 26, following reports that the three militants had first been spotted in the village.
The Pakistan national arrested Sunday was in the village during those searches. At that time, the local man who hosted him had not revealed his guest's nationality to police.