Pakistan is the world’s fifth most populous country, with large segments of its population at risk from non-communicable diseases caused by consumption of harmful products, including tobacco and sugar-sweetened beverages. Even though evidence exists that increased taxes on harmful products leads to consumption reductions as well as increased revenues, Pakistan’s health taxes remain low. We seek to understand the reasons for the deficient health tax regime. Much of the existing literature emphasises industry tactics, resources and motivations. We take a different approach and instead focus on political institutions in Pakistan which could help explain deficiencies in the health taxes regime. We employed a mixed method design. We conducted: (1) a detailed analysis of media content, (2) semistructured interviews with key stakeholders (and attended relevant meetings) and (3) an analysis of primary and secondary literature, including legal and policy documents. We identify two key aspects of Pakistan’s political institutions which may help explain deficiencies in health taxes. First, we identified structural issues in the design and functioning of key institutions responsible for health taxes, including with respect to federalism, intraelite conflict, interagency coordination and intra-agency fragmentation. Second, we found evidence of an entrenchment of industry interests within governmental institutions, which are characterised by weak frameworks for regulating conflicts of interest. We conclude that gaps and conflict within political institutions, owing to weak design, instability and fragmentation, create political opportunity for industry actors to influence the system to advance their interests. The findings of this research indicate towards needed interventions.