An algorithm for calibrating a five-hole Pitot tube in-situ using measurement from a GNSS receiver and IMU is presented. Since GNSS and IMU are standard sensors on most modern aircraft including small UAVs, the algorithm has the promise of simplifying the process of calibrating Pitot tubes by obviating the need for special instrumentation during flight tests. The algorithm is a cascaded, two-stage, batch estimator which uses the ground speed and attitude solution from the fusion of GNSS and an IMU as a reference. A method for the design and analysis of flight test trajectories to yield more accurate calibration results is discussed. The algorithm is validated on the data from the two flight tests, and those tests are conducted using an UltraStick 120 UAV. The mean square error (MSE) of airspeed using the linear method in stage 1 is 0.1278 m/s and 1.0510 m/s for each flight respectively. The error bounds of angle-of-attack and-sideslip in stage 2 are 0.2405 degrees and 0.1476 degrees for Fight Test 1, and 1.3982 degrees and 0.0322 degrees for Flight Test 2 respectively.