Flow rate is one of the important variables for precise motion control and detection of the faults and fluid loss in many hydraulic components and systems. But in many cases, it is not easy to measure it directly. The orifice area of a servo valve by which the fluid flows is one of key factors to monitor the flow rate. In this paper, we have constructed an estimation algorithm for the effective orifice area by using the model of a servo valve cylinder control system and Kalman filter algorithm. Without geometry information about the servo valve, it is shown that the effective orifice area can be estimated by using only displacement and pressure data corrupted with noise. And the effect of the biased sensor data and system parameter errors on the estimation results are discussed. The paper reveals that sensor calibration is important in accurate estimation and plausible parameter data such as oil bulk modulus and actuator volume are acceptable for the estimation without any error. The estimation algorithm can be used as an useful tool for detecting leakage, monitoring malfunction and/or degradation of the system performance.