The invention relates to a device for vacuum stoppering a medical container. The device includes a main body defining an internal volume that has a variable pressure chamber configured to be connected to a vacuum pump. A stopper holder system is arranged in communication with the variable pressure chamber and is configured to receive and hold a stopper aligned with the direction of travel of a piston rod. A piston rod is moveable inside the internal volume of the main body along a longitudinal axis between a proximal rest position and a distal operative position wherein the piston rod pushes the stopper into the medical container. A container holder system provided in the main body, is arranged distally relative to the stopper holder system and in communication with the variable pressure chamber.