Systems Engineering has successfully supported the space industry since its inception with methodologies and techniques to handle complex projects. However, the conventional design approach, ‘Document‐Based Systems Engineering’ (DBSE), is more and more reaching its limits. This research evaluates the benefits and the cost associated with the paradigm of ‘Model Based Systems Engineering’ (MBSE) instead of DBSE by applying the Systems Modelling Language (SysML) in the frame of the Atomic Clock Ensemble in Space (ACES) project. ACES is indeed deemed to be a suitable project for this study as it includes both a very complex ground segment as well as a challenging space segment on board the International Space Station. Following an introduction to SysML and the ACES mission, we first develop the metrics on which the cost‐benefit analysis is based on. Then, we explain the methodology and models used to perform the analysis which targets to characterise DBSE versus MBSE based on the ACES ground segment development. Then, we use the Analytical Hierarchical Process to determine weighted criteria where attention is also given to the transitional process between DBSE and MBSE. After a critical reflection upon the analysis methodology and its results, we focus on lessons‐learned from the use of SysML for the implementation of MBSE in space projects. We have identified five key areas of lessons‐learned for using MBSE with SysML itself as well as main deficiencies for Enterprise Architect, the tool used to implement SysML. We conclude with seven suggested improvements which are considered valuable to help improving the performance and acceptance of MBSE for the development of (space) projects in the future.