Manufacturing enterprises have been doing their best endeavors to obtain competitiveness using various methodologies, such as information technology. In order to achieve competitiveness, they are adopting manufacturing execution system (MES). MES is a total management system that manages from the beginning of the production by product order until the quality inspection of the finished product. And MES is an inter-mediator for supplementation of information gap between ERP and inspection machine and equipment. This paper describes on establishment of effective strategy based on BPR methodology and implementation of MES small and medium PCB manufacturing company with multiple-types of products and mixed process flows. And then we proposed evaluation model based on balanced score card (BSC) for considering non-finance elements as well as finance elements. With evaluation model, we analyzed benefits and effects of MES.