An adaptive estimation method for nonlinear structural deformations is presented. The method is based on the ensemble Kalman filter (EnKF), which can effectively handle nonlinearities in structural models by using the Monte-Carlo simulation. In this study, a self-tuning algorithm for the system noise in the conventional Kalman filter is extended and applied for tuning in the EnKF. To verify the effectiveness of the presented method, a numerical experiment was performed for a deployable frame structure system that contains the typical nonlinearities of space deployable structures, that is, the geometrical nonlinearity in flexible members and the cable nonlinearity resulting from its slackened state.