The present study aims to investigate the process of vacuum generation in a second throat vacuum ejector system employed for the high altitude testing of rocket motors. The study shows that the vacuum generation progresses with four distinct stages during the initial start-up process. The initial stage consists of a gradual evacuation process (first stage) which is followed by a transition region (second stage) in which the pressure starts to drop fastly and eventually leading to a rapid evacuation stage (third stage). This is followed with the reappearance of a gradual evacuation stage (fourth stage) which terminates with the onset of the started mode operation. It is found that the various stages of evacuation are closely linked to the internal shock wave movement in the supersonic nozzle. The gradual evacuation is found to be caused by the relatively large nozzle exit pressure caused by the multiple shock cells in the nozzle. The rapid evacuation occurs due to the sudden movement of the first shock cell to the nozzle exit and the reappearance of the gradual evacuation happens during the transformation of the nozzle jet from an overexpanded to underexpanded state. The parametric studies show that with increase in diffuser convergent cone angle, the contribution of vacuum generation from the fourth stage reduces due to a reduction in the maximum possible jet expansion. A same trend in vacuum generation is observed when nozzle distance from the second throat section of the ejector diffuser reduces. © 2021 Elsevier Masson SAS