Protecting Religiously Affiliated Institutions Act of 2018 (Sec. 2) This bill amends the federal criminal code to modify an existing prohibition on intentionally obstructing, by force or threat of force, a person in the free exercise of religious beliefs. The bill specifies that, with respect to the prohibition, a threat of force includes a threat of force against religious real property. Additionally, it establishes a criminal penalty—a fine, a prison term of up to three years, or both—for a violation that results in damage or destruction to religious real property in an amount that exceeds $5,000. Finally, the bill broadens the definition of "religious real property" to include real property owned or leased by a nonprofit, religiously affiliated organization.