We report a new approach for collecting and deconvoluting the data in Hadamard transform capillary electrophoresis, referred to as fast Hadamard transform capillary electrophoresis (fHTCE). Using fHTCE, total analysis times can be reduced by up to 48% per multiplexed separation compared to conventional Hadamard transform capillary electrophoresis (cHTCE) while providing comparable signal-to-noise ratio enhancements. In fHTCE, the sample is injected following a pseudorandom pulsing sequence derived from the first row of a simplex matrix (S-matrix) in contrast to cHTCE, which utilizes a sequence of twice the length. In addition to the temporal savings provided by fHTCE, a 50% reduction in sample consumption is also realized due to the decreased number of sample injections. We have applied fHTCE to the analysis of mixtures of neurotransmitters and related compounds to yield improved signal-to-noise ratios with a total analysis time under 10 s. In addition, we demonstrate the capability of fHTCE to perform time-resolved monitoring of changes in the concentration of model neurochemical compounds.