Educational robotics is a valuable tool in education and therapy for children with neurodevelopmental disorders (NDD), especially when introduced in activities, combined with gamification and storytelling elements. However, the lack of familiarity of therapists with the technologies involved makes their widespread introduction difficult and leads to case-specific rather than more generalizable methods. In this paper, we present an experimental methodology which provides a guide for the introduction of these elements in therapeutical activities with children with NDD. Providing a common framework reduces the gap between the different expertise of therapists, educators, and engineers. While establishing a common vocabulary and objectives, the methodology provides a guide for designing activities and evaluating their therapeutic effectiveness. We provide an example with a pilot study using a low-cost robot (Ozobot) in a therapeutic environment. Results regarding the children’s task involvement, level of attention, and use of social skills were positive. In addition, the attitude of some children changed throughout the sessions, improving frustration tolerance. The discussion of the pilot study provides clues for improving future implementations of the presented methodology, which serves as a framework for the design of future experiments that include therapeutic activities with educational robotics, gamification, and storytelling.