PurposeThe purpose of this paper is to apply the developed systematic mechanical design methodologies, that are obtained in part I, to investigate their success in designing mechanics of a flexible printed circuit board assembly (PCBA) rework cell.Design/methodology/approachThe decision of soldering and desoldering tool, which is the most critical function of a PCBA rework or remanufacturing cell, significantly influences overall design concept. Therefore, the paper starts by applying the design methodology to the soldering and desoldering function. The same study is repeated for the rest of the sub‐functions but only the results are provided.FindingsAn application of rework machine design methodology for the design of a PCBA rework cell has been made available. In addition to this, the embedded knowledge, such as the requirements list, the function structure, the function/means tree, the weighted objective tree and evaluation chart for the soldering and desoldering function are provided.Practical implicationsThe paper is the first work providing both embedded knowledge and the application of the systematic design methodology for the design of a fully automated flexible PCBA rework cell. The methodology leads rework machine designers in a well‐controlled and structured design environment.Originality/valueThe design methodology can be applied to all functions or targeted on key weighted areas to ensure that the designed rework machine meets the key areas of concerns. Furthermore, the methodology is generic and may be used to develop other complex manufacturing sytems.