We introduce a transformer-based AI model for estimating Doppler velocity from incoherent scatter radar (ISR) spectra. Inspired by Vision Transformers, the model uses a standard transformer encoder adapted for radar data. Trained solely on simulated spectra, it performs well on real data from the Arecibo radar and significantly outperforms the traditional least-squares fitting (LSF) method. This approach is potentially applicable wherever spectral data can be parameterized.