We study the hydrodynamic dispersion (HD) by electroosmotic flow in soft microchannels. Considering a fully developed flow in a slit microchannel of low surface potential and adopting the Taylor dispersion theory, we derive analytical solutions for the solute concentration field and the effective dispersion coefficient. We also conduct numerical analyses to broaden the paper’s scope to high surface potentials and to specify a criterion for the validity of the Debye-Hückel linearization in soft microconduits as well as to investigate the broadening of an analyte band from the time of injection. It is demonstrated that the effective dispersion coefficient of a neutral solute band is generally larger for thicker polyelectrolyte layers (PEL). This means that the hydrodynamic dispersion in electroosmotic flow usually increases by grafting a PEL to the surface. It is, however, possible to reduce the HD dispersion by appropriately altering the channel surface. Furthermore, it is found that higher PEL frictions lead to smaller HD. In addition, unlike rigid channels, a smaller HD is not necessarily achieved for a PEL-grafted microchannel by decreasing the surface potential. Finally, anomalies observed in the electrical potential and velocity distributions of soft microchannels are shown to be caused due to the creation of a triple-EDL within and outside the PEL.