The yeast reporter assay has been widely used in various applications such as detection of endocrine disruptors and analysis of protein-protein interactions by the yeast two-hybrid system. The molecular characteristics of the reporter enzyme are critical determinants for this assay. We herein report the establishment of a novel yeast reporter assay using a secretory luciferase, Cypridina noctiluca luciferase (CLuc), as an alternative to the conventional beta-galactosidase. The CLuc reporter assay in yeast is more sensitive and convenient than the conventional assay. A yeast high-throughput reporter assay was established with a laboratory automation system, and the transcriptional activity of hundreds of yeast promoter fragments was comprehensively determined. Our results indicate that the yeast CLuc reporter assay is a promising tool for large-scale and sensitive analysis in the development of new drugs and in various fields of biotechnology research.