We propose a mechanism which allows one to control the transmission of single electrons through a molecular junction. The principle utilizes the emergence of transmission sidebands when molecular vibrational modes are coupled to the electronic state mediating the transmission. We will show that if a molecule-metal junction is biased just below a molecular resonance, one may induce the transmission of a single electron by externally exciting a vibrational mode of the molecule. The analysis is quite general but requires that the molecular orbital does not hybridize strongly with the metallic states. As an example we perform a density-functional theory analysis of a benzene molecule between two Au(111) contacts and show that exciting a particular vibrational mode can give rise to transmission of a single electron.