Repair materials are the first line of attack against deleterious agents, and clearly, their permeability is highly critical for the durability of parent concrete structure being repaired. In this study, water permeability of a repair mortar was measured at early ages (2–5 days) with and without an applied compressive stress. Hollow-core specimens were used and permeability tests were performed under full flow-equilibrium conditions. Four applied stress levels of 0.3fu, 0.4fu, 0.5fu and 0.6fu were investigated, where fu is the compressive strength of the mortar. Results showed some interesting patterns. For the unstressed specimens, the permeability decreased over time due to hydration. For the stressed specimens, the critical stress level for the mortar investigated was seen to be between 0.4fu and 0.5fu. Up to a stress level of 0.4fu, permeability showed no change due to stress both under during loading or unloading regimes. On the other hand, when the stress reached 0.5fu, the permeability increased dramatically. The permeability increases were even more pronounced at a stress level of 0.6fu. Suggesting that there is still a recoverable part to stress-induced damage, at both stress levels of 0.5fu and 0.6fu, the permeability decreased when the specimen was unloaded.