In this paper we evaluate the research performance of 31 economics departments/institutes in Taiwan in the period of 2008 to 2012. The evaluation is based on journal publications, using the latest journal ranking results in evaluating the performance. Compared to previous studies including Tsaur et al. (2006), the current study puts an emphasis on the quality of research in addition to the quantity. To this end, we use results of journal rankings to construct a quality index which is used to weigh the publication. The results show that when evaluating the unit as a whole, the Institute of Economics at Academia Sinica and the Economics Department of National Taiwan University are ahead of others by a large margin. The economics departments of National Tsing Hua University, National Chengchi University, and Tamkang University also have good performance. If evaluating by per capita output, then the Economics Department of National Cheng Kung University, Research Center for Humanities and Social Sciences of Academia Sinica, Graduate Institute of Industrial Economics of National Central University, and the Institute of Economics of National Sun Yat-sen University also perform well.