The Internet of Things (IoT) is a paradigm thatrefers to the ubiquitous presence around us of physical objectsequipped with sensing, networking and processing capabilitiesthat allow them to cooperate with each other and with theirenvironment to reach common goals. General objectives of IoTare improving the quality of human life and optimizing industrialprocesses, by automating tasks that humans must perform. Suchbenefits are obtained by developing IoT applications. Theheterogeneity and interdisciplinary present in the development ofany IoT application classifies such a task as a SystemsEngineering problem. However, to the best of our knowledge, noSystems Engineering approach to develop IoT applications hasbeen proposed so far. The objective of this paper is to introduce aModel-Based Systems Engineering methodology for IoTapplication development, focusing on the design phase, whichaims at helping organizations to develop IoT applications to fullyachieve the benefits of this new paradigm. The approach iscomprised of a method and a tool, which are aligned with provenconcepts from Systems Engineering and Software Architecture literature.