Magnetic skyrmions, swirling nanometric spin textures, have been attracting increasing attention by virtue of their potential applications for future memory technology and their emergent electromagnetism. Despite a variety of theoretical proposals oriented towards skyrmion-based electronics (that is, skyrmionics), few experiments have succeeded in creating, deleting and transferring skyrmions, and the manipulation methodologies have thus far remained limited to electric, magnetic and thermal stimuli. Here, we demonstrate a new approach for skyrmion phase control based on a mechanical stress. By continuously scanning uniaxial stress at low temperatures, we can create and annihilate a skyrmion crystal in a prototypical chiral magnet MnSi. The critical stress is merely several tens of MPa, which is easily accessible using the tip of a conventional cantilever. The present results offer a new guideline even for single skyrmion control that requires neither electric nor magnetic biases and consumes extremely little energy.