A gradual decrease of the mortality rate of infants and under five in the Philippines was recorded from 1996 to 2013. However, this sign of progress still requires additional efforts to achieve the Millennium Development Goal of reducing the risk. This paper attempts to test empirically the different factors affecting mortality rate of infants and under five in the Philippines, an indicator in gauging health security using a time series data (1996-2013). This will serve as a basis in crafting policies that will critically and efficiently reduce the number of deaths. The average mortality rate of infants and under five was selected as the endogenous variable, Gross Domestic Product per capita and out of the pocket health expenditure were treated as the exogenous variable. Health expenditure total percentage of Gross Domestic Product and average percentage of immunization were the mediating variables. Using structural equation modeling, all these variables were tested for possible complex causality. Result showed that both Average Immunization and Gross Domestic Product per capita significantly affect mortality rate (β=-.510, p<.000; β=-1.340, p<.05). Thus, it is strongly recommended that the country should critically undertake measures to increase Gross Domestic Product per capita and should widen immunization rate. The Health Care Researches are invited to submit their scientific work towards our Nursing and Health Care Journal.