In this paper, eddy current pulsed thermography was used to evaluate ballistic impact damages in basalt-carbon hybrid fiber-reinforced polymer composite laminates for the first time, to our knowledge. In particular, different hybrid structures including intercalated stacking and sandwich-like sequences were used. Pulsed phase thermography, wavelet transform, principle component thermography, and partial least-squares thermography were used to process the thermographic data. Ultrasound C-scan testing and X-ray computed tomography were also performed for comparative purposes. Finite element analysis was used for validation. Finally, an analytical and comparative study was conducted based on signal-to-noise ratio analysis.