A flow rate sensor includes a collision sensing plate and a variable resistance unit. The collision sensing plate is positioned in a flow path of the fluid and is bent with a different degree depending on a flow rate of the fluid. The variable resistance unit is connected to the collision sensing plate, and varies resistance depending on the degree of the bend of the collision sensing plate. A fuel cell system with the flow rate sensor is capable of measuring the flow rate of fluid such as fuel with an inexpensive cost and in a manner of not substantially interrupting the flow of the fluid.