The effect of particle size (50% passing size (D50) of 20 μm, 14 μm and 7 μm) and content (8%, 10% and 12% by mass) of rice husk ash (RHA) on the autogenous shrinkage evolution of high-strength concrete was investigated. RHA samples were selected based on differences in their pore structures, which were investigated by means of nitrogen adsorption isotherms, scanning electron microscopy and absorbency tests. Cement–pozzolan hydration development was studied using isothermal calorimetry. The concretes were subjected to mercury intrusion porosimetry and compressive strength tests. Considering a statistical 22 factorial analysis with a central point, the results showed that D50 and the interaction between D50 and RHA content influenced the autogenous shrinkage at 28 and 100 days. The water absorbed internally by the preserved RHA pore structure (D50 ≈ 20 μm) in the high cement replacement (12% RHA) mixes reduced the final autogenous shrinkage of concrete without a decrease in compressive strength. In addition, the RHA with a more preserved pore structure accelerated the hydration kinetics by heterogeneous nucleation. However, this behaviour did not influence the early autogenous shrinkage results.