The propulsion department is responsible for the propulsion element(s) in the rocket as well as the pyrotechnics in any separation events. In the early years of AQUILO the rocket motor used on AQUILO I and II was one manufactured and designed by DARE (The rocket team of TU Delft). For AQUILO III, the intern Tommy Borsboom designed the PB-51 rocket motor. A custom motor, designed by and for AQUILO with the help from Leo Deelman (NERO). This process was not without its difficulties. AQUILO III's PB-51 experienced structural failure upon ignition resulting in the loss of the launch vehicle. The second attempt, the AQUILO III.V, was from a propulsion standpoint a success. From that point forward, the AQUILO PB-51 has flown several times and has proven to be reliable. Currently, the propulsion department is looking to the future, developing three new motors. Two of which are derivatives of the PB-51: The PB-51B and the PB-82 for use in the AQUILO VIII, and one is a completely new design, the RE-1 for use in the AQUILO VII. The department is also looking into the possibility of hybrid or liquid/gaseous rocket engine designs for the long-term future of AQUILO.

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The propulsion department consists, as every department, of a department head, members and advisors. The current department is shown below. They deal with a workload that is mostly theoretical in nature. Research, calculation and simulation are of paramount importance when working with motors. The department is also responsible for manufacturing and testing the motors.