The Koopman operator allows a nonlinear system to be rewritten as an infinite-dimensional linear system by viewing it in terms of an infinite set of lifting functions instead of a state vector. The main feature of this representation is its linearity, making it compatible with existing linear systems theory. A finite-dimensional approximation of the Koopman operator can be identified from experimental data by choosing a finite subset of lifting functions, applying it to the data, and solving a least squares problem in the lifted space. Existing Koopman operator approximation methods are designed to identify open-loop systems. However, it is impractical or impossible to run experiments on some systems without a feedback controller. Unfortunately, the introduction of feedback control results in correlations between the system's input and output, making some plant dynamics difficult to identify if the controller is neglected. This paper addresses this limitation by introducing a method to identify a Koopman model of the closed-loop system, and then extract a Koopman model of the plant given knowledge of the controller. This is accomplished by leveraging the linearity of the Koopman representation of the system. The proposed approach widens the applicability of Koopman operator identification methods to a broader class of systems. The effectiveness of the proposed closed-loop Koopman operator approximation method is demonstrated experimentally using a Harmonic Drive gearbox exhibiting nonlinear vibrations.