Microelectromechanical system (MEMS) mirror based laser beam scanning (LBS) projectors for fringe projection profilometry (FPP) are becoming increasingly popular attributing to their small size and low cost. However, the initial phase of the scanning MEMS mirror employed in an LBS projector may vary over time, resulting in unstable and distorted fringe patterns. The distorted fringe patterns will largely decrease the accuracy of the three-dimensional (3D) topographic reconstruction. In this paper, an efficient phase delay calibration method based on a unique fringe projection sequence and a corresponding image processing algorithm is proposed. The proposed method can compensate the phase uncertainty and variation with no need to add any extra components. One LBS projector has been constructed using a uniaxial electrostatic MEMS mirror that has a mirror size of 2.5 mm × 2.5 mm and a scanning field of view of 60 ∘ at its resonance of 1523 Hz. 3D reconstruction experiments are conducted to study how the 3D reconstruction results are affected by the phase delay. The standard deviation of a sphere reconstruction is improved from 2.05 mm to 0.20 mm after the positive phase delay deviation of 5 μs is compensated using this new calibration method.