This study is about the calculation of practical orthometric height for permanent GPS station. We presented the method to determine the orthometric height precisely by combining leveling data, GPS data and gravimetry data, and determined the orthometric heights of thirty GPS stations. To test the result we developed the expected error model fur the determined orthometric heights regarding the accuracy of Korean national benchmarks and the precision of surveying methods used at this project. The reliability of the results was presented by comparing it with expected error model statistically.