The seeding of a porous scaffold with stem cells is a fundamental step in engineering sizeable tissue constructs that are clinically viable. However, a key problem often encountered is inhomogeneous seeding of the cells particularly when the cells are delivered through the thickness of the scaffold. To address this problem, different seeding techniques and technology have been investigated. Though few studies have employed computational modeling to theoretically evaluate and characterize available seeding techniques and technology, a transient computational fluid dynamics (CFD) quantification and optimization of an existing clinically viable seeding technique and technology has yet to be reported. The objective of this study was to establish the quantitative relationships between the cell seeding efficiency and the initial vacuum pressure in a compact perfusion seeding device that uses the effect of differential pressure induced by vacuum to seed cells on a porous scaffold. Since fluid flow provides an ideal means of transporting the cells into the scaffold, transient CFD solution of the fluid flow in the cubic configuration of the device was obtained using the initial vacuum pressure recommended in the patent for the device. Subsequently, the initial vacuum pressure was optimized for efficient cell seeding and applied to a cylindrical configuration of the device. Results indicate that the optimal initial vacuum pressure for homogenous cell seeding is approximately −20kPa for both configuration of the seeding device. This optimal initial vacuum pressure is approximately 80% lower than recommended in the patent. This study presents a 3-D computational model that can be employed as part of a systemic stepwise approach to designing and optimizing cell seeding techniques and corresponding technology.