This research aims to examine the difficulties encountered by secondary school students in the mathematical modeling process applied synchronous in online learning environments (OLEs). The research was conducted on 11 8th grade students (8 girls, 3 boys) studying in a public secondary school in Türkiye, using the case study method, by recording audio and videos for 6 weeks. Participants worked collaboratively within a group to complete various problems using the Dynamic Mathematics Software (DMS) GeoGebra. The themes that students had difficulty with in the Online Mathematical Modeling (OMM) process were determined as technical difficulties, access to information and reliability, limited view, shared tasks, limited interaction, time management and time constraints. Using digital tools and instruments in the modeling process offers many advantages to students, however it can also create technical problems. Conspicuous difficulties encountered in the Mathematization and Working Mathematically process is noted, particularly in relation to the DMS. In addition, it was found that the difficulties encountered by students while obtaining information from different sources sometimes negatively affected their solution suggestions. Limitations about the students' interactions with their peers, teachers, and technology during the OMM process caused various difficulties in the stages of the modeling cycle. Future research should focus on developing methods to increase students' interaction and collaboration in OMM processes by overcoming technical difficulties.