This study explored students' perceived metacognition (self-regulation and co-regulation) in relation to the online presence within the Community of Inquiry (CoI) framework in an online case-based instruction (CBI) course. Forty-seven online graduate students enrolled in an instructional design course participated in the study. Data were collected through CoI survey instrument and shared metacognition questionnaire online survey. The findings revealed that students perceived cognitive presence is higher and less variable among three online presences and metacognition in online CBI. The correlation between two interdependent dimensions of metacognition (self-regulation and co-regulation) was significantly high. Also, co-regulation showed stronger relationships with the three online presences (social, teaching, and cognitive) than self-regulation. Additionally, social presence demonstrated the strongest association with both self-regulation and co-regulation, followed by cognitive presence. These results suggest that students with higher perceived social presence tend to have high metacognition. However, students with higher perceived teaching presence are relatively less likely (or unlikely) to have higher metacognition as teaching presence was found to be the most variable among students, which means that teaching presence was perceived differently.