The purpose of this study was to explore instructors' perspectives on the effect of using pen-based technology in the online mathematics courses and understand instructors' experiences in online mathematics teaching with pen-based technology. In this study, two instructors who taught online mathematics courses in fourteen weeks used digital pen as a pen-based technology. The data were obtained from semi-structured interviews and observation of online mathematics course records. The findings indicated that the use of digital pen in the online mathematics course was fairly beneficial in pedagogical and interaction aspects and it was necessary to use digital pen in online mathematics courses for displaying steps of problem solving process synchronously. It was concluded from the study that digital pen technology plays a positive role in the enhancement of interaction between the elements of an online learning environment by providing real-time feedback to students and permitting to digitize mathematical concepts. The observation findings also supported the statements of the instructors. The findings of the study have further provided some insight into how to use digital pen by an instructor in online mathematics course efficiently.