Religious authorities in many Muslim-majority countries have argued that the suspension of communal prayers during an epidemic does not contravene Islamic law. In Pakistan, such measures have proven difficult to enforce, in part because many religious leaders in the country have opposed the closure of places of worship and the limits placed on public religious gatherings. The question is why? This paper suggests that the distrust of the state in matters of religion in Pakistan can be traced back to the colonial era, and that the political developments following independence have amplified frustration and mistrust between political and religious authorities in the country. Significant sources of contention in matters of religion and state remain unresolved under the prime ministership of Imran Khan. At the same time, the pandemic has thrust earlier conflicts into the spotlight and exposed contests over opinion, expertise, and authority in matters of religion and public health.