Pandemic influenza has been considered as a serious international health risk by many health authorities in the world. In mitigating pandemic influenza, effective allocation of limited health resources also plays a critical role along with effective use of medical prevention and treatment procedures. A national resource allocation program for prevention and treatment must be supported with the right allocation decisions for all regions and population risk groups. In this study, we develop a multi-objective mathematical programming model for optimal resource allocation decisions in a country where a serious risk of pandemic influenza may exist. These resources include monetary budget for antivirals and preventive vaccinations, Intensive Care Unit (ICU) beds, ventilators, and non-Intensive Care Unit (non-ICU) beds. The mathematical model has three objectives: minimization of number of deaths, number of cases and total morbidity days during a pandemic influenza. This model can be used as a decision support tool by decision makers to assess the impact of different scenarios such as attack rates, hospitalization and death ratios. These factors are found to be very influential on the allocation of the total budget among preventive vaccination, antiviral treatment and fixed resources. The data set collected from various sources for Turkey is used and analyzed in detail as a case study.