The objective of this study was to investigate the influence of pore geometry on the transport rate and depth after repetitive mechanical deformation of porous scaffolds for tissue engineering applications. Flexible cubic imaging phantoms with pores in the shape of a circular cylinder, elliptic cylinder, and spheroid were fabricated from a biodegradable polymer blend using a combined 3D printing and injection molding technique. The specimens were immersed in fluid and loaded with a solution of a radiopaque solute. The solute distribution was quantified by recording 20 mm pixel-resolution images in an X-ray microimaging scanner at selected time points after intervals of dynamic straining with a mean strain of 8.6 AE 1.6% at 1.0 Hz. The results show that application of cyclic strain significantly increases the rate and depth of solute transport, as compared to diffusive transport alone, for all pore shapes. In addition, pore shape, pore size, and the orientation of the pore cross-sectional asymmetry with respect to the direction of strain greatly influence solute transport. Thus, pore geometry can be tailored to increase transport rates and depths in cyclically deformed scaffolds, which is of utmost importance when thick, metabolically functional tissues are to be engineered.