Selection of capital medical equipment remains unstructured and arduous for hospital managers due its complexity. The aim of this study is to develop a decision support technique that will assist in selection of PET/CT systems using the analytic hierarchy process (AHP) for a department of nuclear medicine in the Czech Republic. The newly build expert group was composed of two physicians, two radiation physicists, and two leading radiology assistants. Selection of the key criteria for alternatives comparison was carried out based on the literature search, technical specifications from completed procurements of PET/CT systems, and preferences of the expert group. Six models of PET/CT systems were included in the study as possible alternatives. The comparison of PET/CT systems was performed using AHP method, where compliance of expert judgements was ensured by Delphi method. Based on the combination of weights assigned to the criteria and results from an evaluation of alternatives, the resulting rank list of PET/CT systems was determined. We have performed a sensitivity analysis to test reliability of the decision. Applied selection procedure and results of this study can serve as an example for the rational selection of medical equipment and could be adjusted according to the needs of specific requirements.