Background: Over the course of the thrombectomy procedure, clot fragments may become dislodged and lead to downstream emboli due to manipulation of an endovascular device. The EmboTrap thrombectomy system features an inner stent channel with an outer stent trap design that may potentially reduce the risk of distal clot fragmentation during clot removal. We tested the hypothesis that distal emboli to both the same and new territory generated during mechanical thrombectomy are a function of device design. Methods: EmboTrap and Solitaire thrombectomy were conducted in an in vitro model system that mimicked a middle-cerebral artery (MCA) occlusion within a complete circle of Willis vascular replica and a contrast-enhanced clot analog. Emboli generated during the procedure with a size >1,000 μm were collected and measured with calipers. The Coulter principle was used to characterize emboli with a size between 200 and 1,000 µm. Results: EmboTrap thrombectomy resulted in a significant reduction in the risk of large emboli (>1,000 μm) formation as compared to first-generation stent retriever thrombectomy (p = 0.031, Fisher exact test). The majority of emboli >1,000 μm (∼80%) were found in the MCA, regardless of device type. There was no significant difference between the EmboTrap and Solitaire in 200 to 1,000 μm emboli formation (p = 0.89, Mann-Whitney test). When combining all emboli in the most dangerous range (>200 μm), EmboTrap offered a size reduction of emboli (p = 0.022). Conclusion: The risk of distal embolization can be altered with improved stent retriever design. When encountering fragment-prone clots, EmboTrap thrombectomy may lower the risk of distal embolization.