Clay core dams are widely applied in reservoir construction, regulating water resource and provide electric power. Leakage is a common problem in reservoir construction, and the leakage amount, which not only affects the economic benefits of the project, but also relates to the safety of the dam body, is difficult to estimate. According to Darcy’s law and stable seepage theory, an analytical method can be proposed to calculate the leakage of the clay core dam to gain the seepage flux in a short time. By making some reasonable assumptions, we propose formulae for seepage calculation in different conditions of the position of the groundwater levels, below or above the reservoir bottom. Both sets of formulae contain two parts of leakage calculation, i.e., leakage from the reservoir bottom and leakage from the dam body. By using the proposed analytical method, the leakage of clay core dams can be estimated considering the influence of the groundwater level. To prove the rationality of the analytical method, a simple numerical model can be established using Geo-studio 2020 to calculate the seepage flux of the clay core dam, where relative errors between numerical solutions and analytical solutions are less than 10%. To verify the feasibility in engineering applications, the proposed method was applied to calculate the seepage of a clay core dam in Sichuan, China, which was also calculated using numerical methods by establishing a three-dimensional model. The results show the rationality of the analytical method, which can strike a balance between precision and efficiency.