There are many techniques for preparing two-dimensional aligned fibril matrices. However, the critical problem associated with these techniques is the destruction of the native structure (e.g., the α-helix) of the proteins. Moreover, most of these techniques cannot create a three-dimensional (3D), aligned reconstituted collagen fibril matrix in one step. In this study, we used a simple device composed of a pneumatic membrane that generates a tunable vibration frequency to apply physical stimulation to fabricate a 3D, aligned collagen fibril matrix with the characteristic D-period structure of collagen in one step. Using second harmonic images, we demonstrated that the aligned, reconstituted collagen fibrils preserve the native collagen D-period structure. The average angular deviation of fibril alignment was reduced to 25.01 ± 4.2° compared with the 39.7 ± 2.19° of alignment observed for the randomly distributed fibril matrix. In addition, the ultimate tensile strength of the aligned matrix when force was applied in the direction parallel to the fiber orientation was higher than that of the randomly oriented matrix. The aligned reconstituted collagen fibril matrix also enhanced the expression of smoothelin (a specific marker of contractile phenotype) of thoracic aortic smooth muscle cell (A7r5) relative to the randomly distributed collagen fibril matrix.