The excellent crack control capability of Engineered Cementitious Composites (ECCs) is exceedingly beneficial for waterproofing applications. To design a suitable ECC matrix for waterproofing applications, waterproofing admixture (WPA) was added to improve the wetting property and reduce the sorptivity, and shrinkage-reducing admixture (SRA) together with calcium sulfoaluminate cement (SAC) were introduced to control the drying shrinkage. A comprehensive experimental program was conducted to optimize the use of WPA, SRA and SAC. Moreover, the water permeability of both un-cracked and cracked ECCs were examined. This work finally developed a kind of waterproof ECC, with 28-day compressive strength around 35 MPa, ultimate tensile strain over 4%, a water contact angle larger than 110 degree, 28-day drying shrinkage about 2/3 the value of the typical ECC (M45), a water absorption rate around 5 × 10−5 mm/s1/2 and a water permeability coefficient about 8 × 10−12 m/s. The findings of this research should be rewarding for the design of ECCs for waterproofing applications.