This paper presents vibration analysis of maskless exposure module in printed circuit board(PCB) manufacturing system. In order to complete exposure process in PCB, masking type module has been widely used in electronics industries. However, masking process confronts some limitations of application due to higher production cost for masking as well as lower printing resolution. Therefore, maskless exposure module is started to be in the spotlight for flexible production system to meet the needs of fabrication in variable patterns at low cost. Since maskless exposure process adopts direct patterning to PCB, vibration problems become more critical compared to conventional masking type process. Moreover, movements of exposure engine as well as stage generate vibration sources in the system. Thus, it is imperative to analyze the vibration characteristics for the maskless exposure module to improve the quality and accuracy of PCB. In this study, vibration analysis using the finite element analysis is conducted to identify the critical structural parts deteriorating vibration performance. Also, Experimental investigations are conducted by single/dual encoder measurement process under the operating module speed. Measurement points of vibration are selected by three places, which are base of stage, exposure engine and top of stage, to check the effect of vibration from the exposure engine. Comparisons between analysis results and experimental measurement are conducted to confirm the accuracy of analysis results including the developed FE model. Finally, this studies show feasibility of optimal design using the developed FE analysis model.