This paper presents a behavior-based protocol study conducted with mechanical engineering students, where the participants developed function–structure models for a novel design problem. A modeling activity video was recorded for each participant and coded using a protocol analysis that captured the modeling sequence, actions, and elements. Pauses in the modeling process were analyzed to identify patterns based on pause time and frequency, the distribution of pauses over the modeling activity, and events preceding and following the pauses. In this study, a pause is characterized as an interruption in the modeling process lasting at least 2 s. Participants were found to spend an average of 38% of the modeling time in pauses, with more of it being allotted to the middle of the modeling activity and less toward the start and end. Three pause types are defined (short, intermediate, and long pauses) based on an analysis of pause lengths, which are then used to analyze events before and after pauses. Participants added elements to the model more frequently, compared to editing and deleting elements. Longer pauses were observed before participants before elements are removed from the model, whereas editing was done more frequently after shorter pauses. Several modeling element pairs are identified that are infrequently separated by pauses, such as the “edge” and “edge text” pair, suggesting that the designer thinks about these as paired elements rather than distinct elements. Limitations of the research methods are discussed, and finally, new research questions are identified as continuing work for this research.