Controlled dehydrogenation of individual trans-2-butene molecules adsorbed on the Pd(110) surface is achieved with inelastically tunneled electrons from the tip of a scanning tunneling microscope (STM). The reaction product is identified as 1,3-butadiene molecule by inelastic tunneling spectroscopy (IETS) using the STM. The reaction yield increases significantly above a threshold bias voltage of ∼366 mV for trans-2-butene and ∼275 mV for fully deuterated trans-2-butene. These coincide with the excitation of C-H and C-D vibrational stretching modes, respectively. The strong isotope effect and the power-law dependence of the reaction rate on the tunneling current explain of the microscopic mechanism for the reaction as vibrational heating via resonant inelastic electron tunneling process.