Emerging research within the field of personalised medicines has aimed to enhance patient treatment through the use of pharmaceutical products that are customised to the individual needs and preferences of the patient. The currently dominant production platforms of pharmaceutical products, however, regard a mass production paradigm and are thus unfeasible for the production and provision of personalised medicines. The production platforms are not designed or are intended for a customisation context. Operating such a context with the current supply chain entails challenges such as increasing costs, time to patient and efforts in quality assurance activities. To address these challenges, this paper presents four reconfigured pharmaceutical supply chain designs. A qualitative operational performance assessment elicits the strengths and weaknesses of the respective supply chain design operating in a customisation context. The results suggest that a later point of variegation, that is, the point in the supply chain where the final customisation is achieved, can relieve the operational effort of the stakeholders in the supply chain while providing the benefits of personalised medicines, that is, an enhanced treatment outcome of the patient. A trade-off remains, however, between the supply chain’s decreased operational effort and degree of necessary reconfigurations, such as introducing new functions to stakeholder operation, reallocating activities to other stakeholders or educating stakeholders.