Hyperspectral imaging that detects 3D spectra-spatial information has been used in a wide range of applications. Among reported techniques, multiplexed spectral imaging with a single-pixel detector provides as a photon-efficient and low-cost implementation; however, the previous spectral modulation schemes are mostly complicated and sacrifice the imaging speed. Here, we propose a fast and compact hyperspectral single-pixel imaging technique based on programmable chromatic illumination. A multi-wavelength LED array modulated by independent carriers achieves stable and accurate spectral modulation up to MHz in a frequency-division multiplexed manner, hence allowing the full use of the spatial light modulation speed. Additionally, we propose a multi-channel deep convolutional autoencoder network to reconstruct hyperspectral data from highly-compressed 1D measurement. Experimental reconstructions of 12 spectral channels and 64 × 64 pixels are demonstrated for dynamic imaging at 12 fps image rate. The proposed imaging scheme is highly extensible to a wide spectrum range, and holds potential for portable spectral imagers in low-light or scattering applications.