Disclosed is a master cylinder for brake systems including a cylinder body having a bore therein, a first and second piston installed in the bore to move forward and backward, and a first hydraulic pressure chamber and a second hydraulic pressure chamber, the first and second hydraulic pressure chambers being divided from each other in the bore. The master cylinder further includes a pressure regulating channel to connect the first hydraulic pressure chamber to second hydraulic pressure chamber to reduce pressure difference between the first hydraulic pressure chamber and the second hydraulic pressure chamber, and a flow control valve provided in the pressure regulating channel to open and close the pressure regulating channel according to the pressure difference between the first hydraulic pressure chamber and the second hydraulic pressure chamber. The first hydraulic pressure chamber is provided with a large hydraulic pressure chamber expanded to an inside of the cylinder body, and a small hydraulic pressure chamber smaller than the large hydraulic pressure chamber.