Vitamin A deficiency (VAD) is a serious and widespread public health problem in the Philippines. Initiated in 1993, the Philippines National Vitamin A Supplementation Program (NVASP) is one of the oldest, most mature and comprehensive of its kind. This paper presents a cost-effectiveness and efficiency analysis of the NVASP and of a hypothetical program of vitamin A fortification of wheat flour that was conducted to inform policymakers as to how to modify the program. Employing a proxy effectiveness indicator of VAD — the intake of <70% of the recommended daily allowance of vitamin A — in a series of simulations using individual child consumption data, the analysis finds that fortification is more efficient in reducing inadequate vitamin A intake (IVAI) compared to the NVASP. Due to the nature of food consumption patterns, however, fortification alone, is not enough. At what is regarded as the maximum politically acceptable fortification level, there will still be 2.2 million (29%) Filipino children aged 12–59 months who will have IVAI. An investigation of the cost and efficiency of geographically targeted supplementation programs reveals that maintaining a universal supplementation program in urban areas and, in rural areas, introducing a targeted program to only the poorest municipalities (where the prevalence of VAD is the highest) will provide a more acceptable public health policy response than fortification alone. Such a policy will reduce incremental direct Government expenditures on vitamin A programs by nearly 20% and will reduce the number of children with IVAI to 900,000 (12%) Filipino children. The paper describes the fortification and supplementation programs, and how their costs were estimated. Lessons for program designers and policymakers in other countries in which vitamin A deficiency constitutes a public health problem are also discussed.