Amplifier-based pump-probe systems, while versatile, often suffer from complexity and low measurement speeds, especially when probing samples require low excitation fluences. To address these limitations, we introduce a pump-probe system that leverages a 60-MHz single-cavity dual-comb oscillator and an ultra-low noise supercontinuum. The setup can operate in equivalent time sampling or in programmable optical delay generation modes. We employ this system to study the wavelength-dependent excited-state dynamics of the non-fullerene electron acceptor Y6, a compound of interest in solar cell development, with excitation fluences as low as 1 nJ/cm2, well below the onset of nonlinear exciton annihilation effects. Our measurements reach a shot-noise limited sensitivity in differential transmission of 3.4·10–7. The results demonstrate the system’s potential to advance the field of ultrafast spectroscopy.