The performance of the gas turbine engines can be improved using variable area nozzle turbine (VANT) in the off-design condition by actively controlling the mass flow rate for various applications of engine. However, VANT demands part clearances to be provided near both the hub and tip of the vane for its mechanical movement. This clearance induces leakage flow and formation of the leakage vortex which interacts with the secondary flow in the vane passage. In this paper, the numerical study is performed on high endwall angle vane geometry of 2nd stage LPT from Pratt and Whitney E3 engine using commercially available CFD tool ANSYS CFX. The effect of free stream turbulence at 0.5%, 5% and 10% is studied along with the change of incidence angle from −10 to +10 on the annular cascade nozzle flow field. The static entropy contour, vorticity contour and total pressure loss coefficient are used to analyzed the flow. The free stream turbulence affects the structure of the vortices within the flow passage. However, no significant change on total pressure loss coefficient is present as turbulence intensity is changed from 0.5% to 5%, but total pressure loss coefficient increases as turbulence intensity is changed to 10%.