The main unmanned aerial vehicles launched from a carrier aircraft onboard navigation system, usually, is a strapdown inertial navigation system. The paper considers the influence of the time synchronization error in the strapdown inertial navigation system transfer alignment on a moving base task. The influence of the time synchronization error, as well as the technique of its estimation, is directly the subject of this study. SINS mathematical models are considered on the basis of error equations, the state vector, including errors of coordinates, linear velocities projections, attitude angular errors of the measuring coordinate system relative to the calculated one, accelerometers and gyro systematic errors components are extended by the angles of misalignment of two systems – unmanned aerial vehicle strapdown inertial navigation system and carrier aircraft navigation system and time delay component. The measurement vector includes the difference of the corresponding output parameters of two systems – carrier aircraft strapdown inertial navigation system or its navigation system and unmanned aerial vehicle strapdown inertial navigation system. A simulation was performed, and state vector estimates were obtained.