Although daily low intensity pulsed ultrasound (LIPUS) treatment has been shown to induce cellular responses supporting bone repair, in vitro studies in 3D models, such as cellseeded scaffolds, are needed to further investigate the underlying cellular mechanisms. This requires well-controlled conditions in an US bioreactor. Computational studies are needed to investigate various effects on US wave propagation influenced by bioreactor configurations, such as reflections at interfaces and wave interference, and optimize the bioreactor design for experimental repeatability. In this study, an enclosed cylindrical sample holder that contained an inner well for placement of a scaffold immersed in culture medium was fabricated by stereolithography 3D printing and combined with an acoustic absorbent material to eliminate the presence of an air-liquid interface perpendicular to the wave propagation path. Finite element simulations conducted in the frequency domain demonstrated that weak standing waves were present within the culture medium, indicating the effects of reflections at solidliquid interfaces within the sample holder, as expected. Focusing on the acoustic pressure at the inner well surface, it was found that the spatially-averaged pressure varied from a maximum to a minimum value as the thickness of the water layer beneath the sample holder was changed. Average pressure values at antinode positions were 2-fold higher than at node positions. A volumeaveraged pressure was calculated within the culture medium corresponding to the region where a scaffold would be centrally located within the bioreactor. It was shown that the thickness of the volume analyzed had a minimal effect on the calculated average pressure. Time-dependent simulations for one complete pulse (i.e. 1 ms) showed that the acoustic pressure in volumes that would be occupied by scaffolds of two different thicknesses (diameter of 8.5 mm and thicknesses of 0.2 or 2.0 mm) reached a stable value after 45 µs, and then remained at that value until the active period of the pulse ceased. Once the active period ended, the acoustic pressure rapidly decreased to a low baseline pressure. Overall, this study showed that the proposed novel bioreactor design provided a controlled environment for the US treatment of a cell-seeded scaffold by removing the air-liquid interface using a custom-designed sample holder and an acoustic absorbent material.