In an era when the importance of Geographic Information Systems (GIS) is ever increasing, users still find them difficult to learn. The issue mainly derives from the fact that GIS interfaces’ learnability hurdles are not lowered for beginner users. Onboarding interaction is a way to tackle this issue, providing proper guidance to novice users the first time they use the software and consequently making it easier for them to learn the system. Throughout this paper, the study proposes a set of guidelines for designing onboarding interaction for assisting novice users utilizing GIS applications. Employing the method of Research through Design, a design prototype is developed through user studies, which in turn was used as a leverage to draw the guidelines as the final outcome of this research. The prototype addresses three different learnability problems of a GIS application identified through user studies and aims to provide design solutions for what users find difficult, important, and lacking in the GIS system. More specifically, the guidelines deal with helping users orient themselves in the application, learn easy functions by practicing them, and understand more complex features through watching instructive video materials.