Abstract: A system for automatic alignment of two pulses is disclosed. The disclosed system is particularly adapted to align the cathode current pulse supplied to a TWT amplifier with the RF exciter pulse so as to improve the efficiency of the TWT amplifier. The system includes a programmable delay circuit for selectively delaying the cathode current pulse after the system trigger. A pulse alignment signal indicates when the two pulses are in alignment. A system controller carries out a calibration algorithm to interatively change the delay while monitoring the alignment signal to determine the calibrated delay setting resulting in pulse alignment. The calibrated delay setting is then stored in memory, and is employed by the controller during the normal operation mode to adjust the programmable delay circuit to the calibrated value.