Methods for generating a multiple-energy X-ray pulse. A beam of electrons is generated with an electron gun and modulated prior to injection into an accelerating structure to achieve at least a first and specified beam current amplitude over the course of respective beam current temporal profiles. A radio frequency field is applied to the accelerating structure with a specified RF field amplitude and a specified RF temporal profile. The first and second specified beam current amplitudes are injected serially, each after a specified delay, in such a manner as to achieve at least two distinct endpoint energies of electrons accelerated within the accelerating structure during a course of a single RF-pulse. The beam of electrons is accelerated by the radio frequency field within the accelerating structure to produce accelerated electrons which impinge upon a target for generating Bremsstrahlung X-rays.