Percutaneous left atrial appendage (LAA) closure using the WATCHMAN device is a novel option for prevention of stroke associated with atrial fibrillation. However, device-related thrombus (DRT) formation is a concern after WATCHMAN implantation and the predictors of DRT still remain unclear. We aimed to clarify the predictors of DRT after WATCHMAN implantation by analyzing 78 patients (50 males, 72 ± 8 years, average CHA2DS2-VASc score of 4.3 + 1.8) who had undergone WATCHMAN implantation. WATCHMAN was successfully implanted in all patients and four (5%) developed DRT. Patients with DRT were more often female (75 vs. 34%, p = 0.094). CHA2DS2-VASc score was higher for patients with DRT (6.3 ± 2.5 vs. 4.2 ± 1.7, p = 0.022). Chronic kidney disease (100% vs. 43%, p = 0.024) and deep implantation of the device, which was defined as implant position below the LAA ostial plane (75 vs. 24%, p = 0.026), were more common in patients with DRT. HAS-BLED score (4.5 ± 1.0 vs. 3.5 ± 1.1, p = 0.074) was higher and oral anticoagulants (50 vs. 84%, p = 0.086) were less commonly prescribed for patients with DRT. Multivariable logistic regression analysis showed that higher CHA2DS2-VASc score (p = 0.022, OR 2.8) and deep implantation (p = 0.032, OR 24.7) were associated with DRT. These results suggest the possible role of CHA2S2-VASc scores and implantation depth in the development of DRT after percutaneous LAA closure using the WATCHMAN device.