Tobacco use remains persistently high across South Asia, despite numerous public health efforts, and continues to significantly contribute to the burden of non-communicable diseases (NCDs) such as cardiovascular disease, hypertension, diabetes, and stroke. Community pharmacists-widely accessible and trusted within their communities-are an underutilized resource for delivering public health interventions. Graphic health warnings (GHWs), recommended by the World Health Organization (WHO), have been shown to promote smoking cessation, but are rarely paired with personalized counseling by healthcare providers. This study aims to evaluate both the effectiveness and cost-effectiveness of integrating GHWs with pharmacist-led personalized counseling at primary healthcare pharmacies in Bangladesh and Pakistan. A cluster randomized controlled trial (RCT) will be conducted, enrolling 5,052 adult participants in each country from community pharmacies. Participants will be randomly assigned to one of three groups: (1) GHW-only intervention, (2) combined GHW and pharmacist-led counseling, or (3) standard care (control). The intervention includes twice-yearly counseling sessions-delivered both in-person and digitally-supported by educational booklets and leaflets. Primary outcomes are smoking cessation rates and blood pressure reduction. Secondary outcomes include improved hypertension and diabetes management, medication adherence, lifestyle modification, reduced hospitalizations and mortality, and incremental cost-effectiveness. Bayesian statistical models will be used to assess efficacy, and economic evaluations will determine the cost-effectiveness of the interventions. The findings aim to inform scalable public health strategies for tobacco control and NCD prevention in resource-limited settings.