The latest raid came after "several" JeM activists were arrested following leads provided by India over the alleged involvement of the outfit in the Pathankot air base attack.
The raid was launched by Punjab's Counter-Terrorism Department (CTD), one of its officials said.
"No arrest was made but some books, CDs and copies of national identity cards of some suspects were confiscated," he added.
The madrassa was also sealed after a thorough search.
Pakistan has promised India of tough action against anyone found guilty of involvement in the Pathankot attack.
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All the six attackers were killed by the security forces.
Prime Minister Nawaz Sharif yesterday chaired a high- level meeting which was told that offices of JeM were being traced and sealed.
Also yesterday, Pakistani media reported that JeM chief Maulana Masood Azhar, his brother and "several individuals" belonging to his dreaded outfit have been detained after India demanded action. However, the reports of Azhar's detention turned out to be false.