The use of Supply Chain Management (SCM) systems allows for the improvement of an organization’s operations. Companies use many Enterprise Resource Planning (ERP) systems that also include SCM functionalities. As a result, the selection of the right system to be used in the enterprise is a complex problem. The use of multi-criteria decision aid (MCDA) methods provides the possibility of system ordering in a ranking, based on an asymmetric preference relation, symmetric indifference and incomparability relations. The aim of the article is to evaluate ERP systems in terms of their support for SCM. The scientific contribution of the article is the study of the impact of various degrees of uncertainty of the decision-maker’s preferences on the evaluation results and the analysis of the impact of various approaches to the preferences of alternatives on the final ranking. An approach based on MCDA Preference Ranking Organization Method for Enrichment Evaluation (PROMETHEE) was used for the study. The decision model uses 12 criteria, three different preference functions and two variants of the PROMETHEE method (I and II). In this way, a total of six rankings were built, and each of them includes seven systems, supporting the management of the supply chain. As a result of the study, it was found that the highest functionality in logistics is characterized by the Oracle E-Business Suite system, which is more functional than SAP ERP and JD Edwards EnterpriseOne. The remaining analysed systems offer much less functionality. The applied approach, which was possible with the use of various preference functions, allowed three different levels of uncertainty in the preferences of decision-makers to be taken into account in the study. Moreover, the application of two different variants of the PROMETHEE method made it possible for the obtained solution to take into account the uncertainty of positions taken by individual ERP systems in the final rankings.