Scintillation effects are not negligible in the stratosphere. We present a model based on a 3D model of anisotropic and isotropic refractive index fluctuations spectra that predicts scintillation rates within the so-called small perturbation approximation. Atmospheric observations of stellar scintillation made from the AMON-RA (AMON, Absorption par les Minoritaires Ozone et NO(x); RA, rapid) balloon-borne spectrometer allows us to remotely probe wave-turbulence characteristics in the stratosphere. Data reduction from these observations brings out values of the inner scale of the anisotropic spectrum. We find metric values of the inner scale that are compatible with space-based measurements. We find a major contribution of the anisotropic spectrum relative to the isotropic contribution. When the sight line plunges into the atmosphere, strong scintillation occurs as well as coupled chromatic refraction effects.