The fractional Fourier transform (FrFT), a fundamental operation in physics that corresponds to a rotation of phase space by any angle, is also an indispensable tool employed in digital signal processing for noise reduction. Processing of optical signals in their time-frequency degree of freedom bypasses the digitization step and presents an opportunity to enhance many protocols in quantum and classical communication, sensing, and computing. In this Letter, we present the experimental realization of the fractional Fourier transform in the time-frequency domain using an atomic quantum-optical memory system with processing capabilities. Our scheme performs the operation by imposing programmable interleaved spectral and temporal phases. We have verified the FrFT by analyses of chroncyclic Wigner functions measured via a shot-noise limited homodyne detector. Our results hold prospects for achieving temporal-mode sorting, processing, and superresolved parameter estimation.