This study investigated the effect of the incorporation of the supplementary cementitious material (SCM) of hydrophobic silica and silica fume on the mechanical properties and hydration behavior of ordinary Portland cement (OPC). Silica fume is a well-known SCM owing to its good compatibility with OPC by providing seeding sites for nucleation and subsequent acceleration and reactive silica for pozzolanic reaction. This study revealed that mortars containing hydrophobic silica developed higher compressive strength than pure mortar and mortar with regular silica fume during all curing ages. Furthermore, it was confirmed that it contributed to produce more hydration products and consume more portlandite, implying its acceleration and pozzolanic reaction, respectively. Although its particle size is larger than that of silica fume, its hydrophobicity accelerated the hydration reaction due to the better dispersion of OPC in the system, which leads to more exposure of cement particles to available water. These effects could cause higher dissolution of the particles and faster interfacial precipitation of hydration products. Therefore, the hydrophobic silica outperformed the seeding-based acceleration effect of silica fume.