Immobilization systems and their corresponding setup errors influence the clinical target volume to the planning target volume (CTV-PTV) margins, which is critical for hypofractionated prostate stereotactic body radiotherapy (SBRT). This preliminary study evaluates intrafraction prostate displacement for two immobilization systems (A and B). Six consecutive patients having localized prostate cancer and implanted prostate marker seeds were studied. Planar X-ray images were acquired pre-and post-treatment to find the intrafraction prostate displacement. The average absolute displacements (lateral, longitudinal, vertical) were 0.9 ± 0.4 mm, 1.7 ± 0.1 mm, 1.3 ± 0.3 mm (system A), and 0.5 ± 0.2 mm, 0.6 ± 0.1 mm, 0.8 ± 0.3 mm (system B), with average three-dimensional displacements of 2.6 ± 0.2 mm (system A) and 1.3 ± 0.2 mm (system B). The computed CTV-PTV margins (lateral, longitudinal, vertical) were 2.5 mm, 2.5 mm, 3.6 mm and 1.4 mm, 1.6 mm, 2.4 mm for systems A and B, respectively. This suggests that the immobilization system influences intrafraction prostate displacement and, therefore, the margins applied. However, the margins found for both systems are comparable to the margins used for hypofractionated prostate SBRT.