Hydrophobic silane hinders internal water penetration by tuning the surface wettability of concrete. The presence of hydrophobic groups in the silane was observed to adversely influence early cement hydration. This study employs a combination of calorimetry, X-ray diffraction (XRD), thermogravimetric analysis (TGA), scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), inductively coupled plasma optical emission spectroscopy (ICP-OES), and total organic carbon (TOC) analysis to investigate the effects of hydrophobic isobutyl-triethoxysilane (IBTEO) on cement hydration. The results demonstrate that the silicate reaction integral to cement hydration slows as the concentration of hydrophobic silane increases. The nucleation of hydration products, such as calcium silicate hydrate (C–S–H), exhibits heightened sensitivity to the presence of hydrophobic silane. Although hydrophobic silane marginally impacts the initial dissolution of cement particles, it significantly decreases ion dissolution after 60 min. This reduction in hydration rate and the consequent delay in the emergence of the second exothermic peaks in hydration are attributable to the negative impact of the hydrophobic functional groups on the silicate reactions and the formation of hydrogen bonds. These findings offer new perspectives on the impact of hydrophobic silanes on cement hydration, potentially guiding the development of silane-cement systems towards enhanced superhydrophobicity and improved permeability.