This work investigated the effect of hydroxyapatite (HA) nanorods on the strength development and hydration of cement. Undispersed HA nanorods (HA-UD) and dispersed HA nanorods (HA-DN) were prepared by atom-efficient neutralization. The strength of mortars modified by HA nanorods was tested, as well as their compatibility with supplementary cementitious material. The hydration of HA-modified cement pastes was characterized via in situ X-ray diffraction, isothermal calorimetry and scanning electron microscopy. As the results suggest, the undispersed HA-DN caused a considerable increase in superplasticizer demand to achieve the same level of flow. Both HA nanorods showed a significant accelerating effect on early hydration, with approximately 100% strength enhancement at 12 h at 2.0% dosage. The effect on early strength of the nanorods is retained in systems with up to 30% fly ash in the binder mass. According to the characterizations, the rate of the hydration reaction in the acceleration period was enhanced by HA nanorods, and C3S consumption was also increased. In all of the testing situations, HA-DN showed superior performance, likely due to improved spatial distribution of the hydroxyapatites. The results suggest that proper dispersion of the nanorods is necessary to optimize its performance.