We perform a detailed theoretical and experimental investigation of supercontinuum generation in large-mode-area photonic crystal fibers pumped by a high-energy, high-repetition rate picosecond Nd:YVO4 laser, with the goal of using it as the Stokes beam in coherent anti-Stokes Raman scattering setup. We analyze the influence of fiber structure and length on the supercontinuum power, spectral shape, and group delay dispersion. We identify the experimental conditions for stable supercontinuum generation, with microjoule-level pulse energy and the spectrum extending beyond 1600 nm, which allows excitation of Raman frequencies up to 3000 cm−1 and beyond. We demonstrate reliable and efficient operation of a coherent anti-Stokes Raman spectroscopy and microscopy setup using this supercontinuum source.