Abstract Ionospheric scintillation driven by plasma irregularities disrupts radio propagation across frequencies from HF to L‐band. While phase‐screen methods dominate scintillation modeling, they can be inadequate in the E‐region where irregularity scales can be comparable to the radio wavelength or Fresnel scale and span orders of magnitude. Here we quantitatively evaluate scintillation with a new full‐wave methodology coupling particle‐in‐cell simulations of the gradient drift (GD) and Farley‐Buneman instabilities with finite‐difference time‐domain electromagnetic propagation. Using a frozen‐in approximation and spatial filtering, we evaluate the contributions of various turbulence scale sizes to HF (6–24 MHz) phase and amplitude scintillation. Long‐wavelength GD waves dominate the modeled amplitude scintillation through diffractive scattering, while Farley‐Buneman turbulence contributes negligibly. Amplitude spectra closely follow irregularities near the Fresnel scale, demonstrating a direct correspondence between scintillation and plasma structuring. These results demonstrate full‐wave scintillation modeling and provide a framework for investigating scintillation across a wide range of spatial scales.