The growing need for solutions that can support the computer-based and distant assessment of functional models has resulted in ad hoc implementations of various diagramming tools. These tools are typically not intended for the purpose of functional modelling and lack the flexibility and efficiency of the traditional pen-and-paper approach. This paper reports on an experimental study of 42 students who were introduced to functional modelling through either printed vocabulary materials for pen-and-paper modelling or a specifically developed software application for computer-based modelling. All participants received an identical task—model an electric citrus juicer—with a brief description of how one operates and a photograph of a commercial example. The results show no significant difference in their total scores. However, the pen-and-paper group performed significantly better when it came to the selection of appropriate functions and creating plausible function–flow pairs. These results suggest that the current version of the software alters the functional modelling process in which the students typically engage. Also, it has been hypothesised that the software tool’s lack of flexibility and dynamism in presenting the predefined function vocabulary, when compared to the traditional printouts, might result in earlier fixation and the selection of less appropriate functions. On the other hand, the computer-supported approach can be better controlled and is less prone to critical errors, such as disregarding functional modelling conventions.