Background: We investigated the size-based isolation and enumeration of circulating tumor cells (CTCs) using a centrifugal microfluidic device equipped with fluid-assisted separation technology (FAST disc) and demonstrated the correlation among CTC count, CA125, and the clinical course. Methods: We prospectively recruited 13 women with ovarian cancer between December 2016 and August 2018 at Keimyung University Dongsan Hospital. We collected 49 serial blood samples at multiple time-points. CTCs were isolated from whole blood using the FAST disc and were defined as EpCAM+, cytokeratin+, CD45−, and DAPI+. Results: We successfully achieved the high-throughput, efficient, and label-free isolation of CTCs from the blood of ovarian cancer patients using FAST discs. The mean and median CTC count were 20.2 and 6.0, respectively, and 84.62% patients (11/13) had more than 1 CTC at baseline and a decreased CTC count after surgery and chemotherapy, except for 2 patients who had no CTCs at baseline. The median follow-up duration was 22.7 months. At the time of complete response, CTC count in 8 patients was <3. CTC count was correlated with CA125 in 3 patients with no recurrence but elevated in 3 patients with recurrence and normal range of CA125. CTC count and CA125 had high concordance with directional change (increasing 71.4% and decreasing 75.0%). CTC count showed higher association with the clinical status and higher sensitivity (100.0% vs. 60.0%), positive predictive value (55.6% vs. 42.9%), and negative predictive value (100.0% vs. 87.5%) than CA125.Conclusions: CTC count was better associated with treatment response and recurrence than CA125.