Green buildings have been widely adopted to achieve sustainable development in the built environment. However, the high cost is the main obstacle to develop green buildings. Whether the operational savings of green buildings could recover the initial construction cost is still under debate. This paper aims to empirically examine the above question by conducting a life cycle cost analysis of non-residential green buildings in the tropic climate by comparing the Life Cycle Costs (LCC), Construction Costs (CC) and Operation Costs (OC) for various types of buildings that are certified by different levels of Green Mark in Singapore. Data were collected from 44 non-residential buildings that were constructed over the period for 1978–2013 on a national scale. The findings show that the annualized average values of LCC, CC and OC of green buildings are S$ 222.03/m2, S$ 91.85/m2 and S$ 130.18/m2 respectively (S$ as Singapore Dollar, $ as United States Dollar, and S$ 1 = $ 0.73). One level increase of the Green Mark certificate standard would increase the annualized LCC and CC by S$ 47.81/m2 and S$ 25.37/m2 respectively, with no significant influence on the OC. Key influencing factors and their effects on both the annualized LCC and OC have also been identified in the discussion. The findings contribute to the literature by providing a clear framework to analyze life cycle economic assessment of green buildings and by enriching the diversity of cost comparison for green buildings across different regions.