Engineered Cementitious Composite (ECC) is a family of high performance fiber reinforced cementitious composites featuring strain-hardening behavior and high tensile ductility (with tensile strain capacity of 3–5%). ECC achieves high ductility by forming multiple microcracks with crack width less than 60 μm under tension. The tight crack width of ECC naturally lends itself to low permeability even in the cracked stage. Such properties are of particular interest to hydraulic structure applications. In addition to the tight crack width, self-healing of microcracks further lowers the permeability of cracked ECC, enhancing the durability and safety of hydraulic structures. In this paper, the permeability of ECC composites under the influence of self-healing was experimentally studied. Single crack permeability tests were also conducted to directly correlate the permeability and self-healing behavior of a single crack with a given initial crack width. Additionally, an analytical model capable of predicting the permeability of ECC composites that undergo self-healing process is proposed and verified with experimental data. The research findings in the present paper can be used to accurately estimate the permeability of ECC and are expected to provide support for future design and application of ECC for hydraulic structures.