Disclosed is a method for isolating stem cells. The method uses a specially designed apparatus including: a container containing an aspirate; a piston having an outer diameter corresponding to the inner diameter of the container and having at least one through-hole; and a connection tube adapted to feed an enzyme or a washing solution into the container through the through-hole, having a tip connected to the through-hole, and connected to an external tube or another container containing the enzyme or washing solution at the other end thereof. The method includes pulling the piston backward to form a negative pressure in the container containing the aspirate and to allow the enzyme or washing solution to enter the container containing the aspirate through the connection tube and the through-hole of the piston.