In recent automated manufacturing systems, compressed air-based pneumatic cylinders have been widely used for basic perpetration including picking up and moving a target object. They are relatively categorized as small machines, but many linear or rotary cylinders play an important role in discrete manufacturing systems. Therefore, sudden operation stop or interruption due to a fault occurrence in pneumatic cylinders leads to a decrease in repair costs and production and even threatens the safety of workers. In this regard, this study proposed a fault detection technique by developing a time-variant deep learning model from multivariate sensor data analysis for estimating a current health state as four levels. In addition, it aims to establish a real-time fault detection system that allows workers to immediately identify and manage the cylinder’s status in either an actual shop floor or a remote management situation. To validate and verify the performance of the proposed system, we collected multivariate sensor signals from a rotary cylinder and it was successful in detecting the health state of the pneumatic cylinder with four severity levels. Furthermore, the optimal sensor location and signal type were analyzed through statistical inferences.