The man said that while he can call himself a Muslim in the US, he cannot do so in Pakistan for fear of punishment.
"We have never retaliated (against anyone) and have left everything to God. I pray that may God reward you and give you a long life," the man told Trump.
The brief conversation took place as Trump met with victims of religious persecution from various countries at the White House.
The Ahmadiyya or the Ahmadiyya Muslim Jama'at is an Islamic religious movement founded in Punjab, in then British India, near the end of the 19th century. However, Pakistan's Constitution has declared the community as "non-Muslims."
Most of the Ahmadis reside in Rabwah in Punjab province, which is one of the few places in Pakistan having the highest concentration of the community.
The Pakistan Penal Code subjects Ahmadis to severe legal restrictions and officially-sanctioned discrimination, making it criminal for the people of the community to call themselves Muslims, preach, propagate or disseminate materials on their faith, or refer to their houses of worship as mosques.
The Pakistan government applies the anti-terrorism law as an unwarranted pretext to arrest members of the Ahmadiyya community.
Ahmadis also continue to be murdered in religiously-motivated attacks that take place with impunity.