This paper reconciles diverse efficiency measures to characterize the operating performance of the National Innovation System (NIS) in 33 Asian and European countries. NIS efficiency rating should be considered as a key element for achieving greater innovation and competitive advantages. This study applies the data envelopment analysis (DEA) approach with the traditional DEA models, bilateral models, and critical performance measures, respectively, combing multiple outputs and inputs to measure the magnitude of performance difference between the countries. Empirical results indicate that the overall technical inefficiencies of the NIS activities in these countries are primarily due to the pure technical inefficiencies rather than the scale inefficiencies. Korea and Taiwan perform very well on their NISs and rank numbers 1 and 2 respectively on the Asian list, while Romania ranks number 1 among the European countries. In addition, the Asian countries are generally better performers than the European countries in production activities. Finally, the key input/output influencing the countries' NIS performance have been identified. The innovative features of Korea, Taiwan and Romania are also discussed.