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A major limitation of transient optical spectroscopy is that relatively high laser fluences are required to enable broadband, multichannel detection with acceptable signal-to-noise levels. Under typical experimental conditions, many condensed phase and nanoscale materials exhibit fluence-dependent dynamics, including higher order effects such as carrier–carrier annihilation. With the proliferation of commercial laser systems, offering both high repetition rates and high pulse energies, have come new opportunities for high sensitivity pump-probe measurements at low pump fluences. However, experimental considerations needed to fully leverage the statistical advantage of these laser systems have not been fully described. Here, we demonstrate a high repetition rate, broadband transient spectrometer capable of multichannel shot-to-shot detection at 90 kHz. Importantly, we find that several high-speed cameras exhibit a time-domain fixed pattern noise resulting from interleaved analog-to-digital converters, which is particularly detrimental to the conventional “ON/OFF” modulation scheme used in pump-probe spectroscopy. Using a modified modulation and data processing scheme, we achieve a noise level of 10−5 in 4 s for differential transmission, an order of magnitude lower than for commercial 1 kHz transient spectrometers for the same acquisition time. We leverage the high sensitivity of this system to measure the differential transmission of monolayer graphene at low pump fluence. We show that signals on the order of 10−6 OD can be measured, enabling a new data acquisition regime for low-dimensional materials.