During embryonic development, hemodynamic forces caused by blood flow support vascular remodeling, arterialization of luminal endothelium, and hematopoietic stem cell (HSC) emergence. Previously, we reported that fluid shear stress plays a key role in stimulating nitric oxide (NO) signaling in the aorta-gonad-mesonephros (AGM) and is essential for definitive hematopoiesis. We employed a Dynamic Flow System modified from a cone-and-plate assembly to precisely regulate in vitro exposure of AGM cells to a defined pattern of laminar shear stress. Here, we present the design of a microfluidic platform accessible to any research group that requires small cell numbers and allows for recirculation of paracrine signaling factors with minimal damage to nonadherent hematopoietic progenitors and stem cells. We detail the assembly of the microfluidic platform using commercially available components and provide specific guidance in the use of an emerging standard in the measurement of embryonic HSC potential, intravenous neonatal transplantation.