In order to achieve sonic boom reduction in real-world atmosphere, we investigate the effects of uncertainties in atmospheric turbulence and numerical weather prediction (NWP) models on sonic boom. We simulate sonic boom propagation of the Drop test for the Simplified Evaluation of Non-symmetrically Distributed sonic boom (D-SEND) #2 flight test, which was conducted by the Japan Aerospace Exploration Agency (JAXA), using the Tohoku University Xnoise (TUXnoise). TUXnoise is a sonic boom analysis tool based on the Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation and capable to consider diffraction, axial convection, and transverse convection effects induced by atmospheric turbulence. First, the sonic boom propagation is simulated with different transverse size of the simulation domain, which is related to the reproducibility of the effects of atmospheric turbulence. The results indicate that the simulation requires a sufficiently large domain size for a good agreement with the measurement in D-SEND#2 flight test. Second, the sonic boom propagation is simulated under the atmospheric uncertainties such as temperature, humidity, and wind velocity uncertainties estimated by ensemble forecast. The results indicate that wind velocity uncertainty can affect sonic boom significantly through a consideration of atmospheric turbulence. They also indicate that the effect of humidity uncertainty on minimum peak pressure is small because the relaxation effects in the KZK equation depend on humidity and inactive in rounded sonic boom signatures, which result in minimum peak pressure. In addition, it is confirmed that the effects of atmospheric turbulence can change significantly even with a slight change of the propagation path. Finally, the sonic boom propagation is simulated with different atmospheric boundary layer (ABL) height (ABLH). Atmospheric turbulence is assumed to exist in ABL. The results indicate that ABLH must be estimated carefully to evaluate sonic boom properly because the sonic boom is affected more significantly as ABL is thicker. They also indicate that wind shear layers over ABL can be other factors to produce atmospheric turbulence and affect the sonic boom signature when D-SEND#2 flight test was conducted. Hence, the uncertainties in atmospheric turbulence and NWP models must be carefully taken into account for more accurate simulation of sonic boom propagation.