A fully penetrating cut-off wall is a vertical seepage barrier that fully penetrates an aquifer and is embedded in an underlying aquitard to a certain depth. Groundwater seepage with this type of wall occurs through three paths: leakage through the body of the wall in the aquifer, leakage through the body of the wall embedded in the aquitard, and seepage under the wall. Seepage through the first path can be simply treated as one-dimensional flow. However, due to the mutual influence of seepage through the latter two paths, the seepage problem is complicated and still needs to be studied. An analytical method is proposed to solve this problem in this study. Mathematic expressions for flow rate and head value are obtained by superposition of drawdowns of two exact models, namely, the model with only leakage through the wall body and the model with only seepage under the wall, respectively. Exact solutions are quoted or derived for the exact models, but they involve Legendre’s elliptic integrals of the first and third kinds. To facilitate an engineering application, approximate models of the exact models are introduced and their solutions are applied to the analytical formulas. The accuracy and applicability of the proposed method are verified compared with the numerical method. The proposed method provides a simple but effective method for quickly estimating the quantity of seepage in the aquitard (including leakage through the wall body and seepage under the wall) when simultaneously considering the effects of wall permeability and thickness.