Free-standing Si films have been and remain an excellent example to study experimentally the effect of the reduction of the characteristic size on the phonon dispersion relation. A step further in geometrical complexity and, therefore, in increasing the control and manipulation of phonons is achieved by introducing periodicity in the medium to form phononic crystals. Here we report on the development of the fabrication process of large-area, solid-air and solid-solid two-dimensional phononic crystals, directly on free-standing, single crystalline silicon membranes. The patterning of the membranes involved electron-beam lithography and reactive ion etching for holes or metal evaporation and lift-off for pillars. The fabrication was possible due to the external strain induced on the membrane in order to reduce the buckling, which is typically found in large area free-standing structures. As a result, we obtained 250 nm thick structured membranes with patterned areas up to 100 × 100 μm, feature size between 100 and 300 nm and periodicity between 300 and 500 nm. The changes in dispersion relations of hypersonic acoustic phonons due to nanopatterning in free-standing silicon membranes were measured by Brillouin light scattering and the results were compared with numerical calculations by finite elements method. Information on phonon dispersion relation combined with a reliable fabrication process for large-scale structures opens a way for phonon engineering in more complex devices.