The properties of graphene oxide (GO)-based cement paste can be significantly affected by the state of GO dispersion. In this study, the effects of uniformly dispersed and re-agglomerated GO on the rheological, mechanical properties and microstructure of cement paste were systematically investigated. Two distinct dispersion states can be achieved by altering the mixing sequence: Polycarboxylate-ether (PCE) mixed with GO-cement or cement mixed with GO-PCE. The experimental results showed that the yield stress and plastic viscosity increased with the uniformly dispersed GO when compared to those of re-agglomerated GO cement paste. Moreover, the 3-day compressive and flexural strengths of uniformly dispersed GO paste were 8% and 27%, respectively, higher than those of re-agglomerated GO pastes. The results of X-ray diffraction, Fourier transform infrared spectroscopy and scanning electron microscopy analyses demonstrated that uniformly dispersed GO more effectively promotes the formation of hydration products in hardened cement paste. Furthermore, a porosity analysis using mercury intrusion porosimetry revealed that the homogeneous dispersion of GO can better inhibit the formation of large-size pores and optimize the pore size distribution at 3 and 7 days than the re-agglomerated GO.