This paper presents an unsteady flow analysis of a 3D wing with a morphing trailing edge flap (TEF) and a seamless side-edge transition between the morphed and static parts of a wing by introducing an unsteady parametrization method. First, a 3D steady Reynolds-averaged Navier–Stokes (RANS) analysis of a statically morphed TEF with seamless transition is performed and the results are compared with both a baseline clean wing and a wing with a traditional hinged flap configuration at a Reynolds number of 0.7 × 106 for a range of angles of attack (AoA), from 4° to 15°. This study extends some previous published work by examining the inherent unsteady 3D effects due to the presence of the seamless transition. It is found that in the pre-stall regime, the statically morphed wing produces a maximum of a 22% higher lift and a near constant drag reduction of 25% compared with the hinged flap wing, resulting in up to 40% enhancement in the aerodynamic efficiency (i.e., lift/drag ratio). Second, unsteady flow analysis of the dynamically morphing TEF with seamless flap side-edge transition is performed to provide further insights into the dynamic lift and drag forces during the flap motions at three pre-defined morphing frequencies of 4 Hz, 6 Hz, and 8 Hz, respectively. Results have shown that an initially large overshoot in the drag coefficient is observed due to unsteady flow effects induced by the dynamically morphing wing; the overshoot is proportional to the morphing frequency which indicates the need to account for dynamic morphing effects in the design phase of a morphing wing.