The ability to meet increasingly personalized market demand in a short period of time and at a low cost can be regarded as a fundamental principle for industrialized countries’ competitive revival. The aim of Industry 4.0 is to resolve the long-standing conflict between the individuality of on-demand output and the savings realized through economies of scale. Significant progress has been established in the field of Industry 4.0 technologies, but there is still an open gap in the literature regarding methodologies for efficiently manage the available productive resources of a manufacturing system. The CONtrolled Work-In-Progress (CONWIP) production logic, proposed by Spearman et al., allows controlling the Work-In-Progress (WIP) in a production system while monitoring the throughput. However, an affordable estimation tool is still required to deal with the increased variability that enters the current production system. Taking advantage of recent advances in the field of machine learning, this paper contributes to the development of a performance estimation tool for a production line using a deep learning neural network. The results demonstrated that the proposed estimation tool can outperform the current best-known mathematical model by estimating the throughput of a CONWIP Flow-Shop production line with a given variability and WIP value set into the system.