Transient brain-wide neuroimaging on a microscopic scale is pivotal for brain research, yet existing imaging modalities face challenges in meeting such spatiotemporal requirements. Functional ultrasound (fUS) enables transient neurovascular imaging through red blood cell backscattering, but suffers from diffraction-limited spatial resolution. Functional ultrasound localization microscopy (fULM) has addressed this limitation by integrating ULM with fUS; but this approach requires repeated stimulation and data accumulation. Here, we introduce super-resolution functional ultrasound (SR-fUS), a deep learning-based framework that reconstructs super-resolution ULM images from contrast-free ultrafast Doppler data. By incorporating red blood cell radial gradient fluctuation priors with uncertainty-driven loss, SR-fUS enables microscopic scale hemodynamic imaging with 25-μm spatial spatial resolution. In rat brains, SR-fUS visualized transient pain-evoked hemodynamic responses, distinguished stimulus-specific microvascular activation patterns during single-whisker stimulation, and dynamically tracked isoflurane anesthesia-induced microvascular dilation. The accuracy of SR-fUS was further preliminarily assessed through a comparative study with two-photon microscopy.