This paper presents the design of ultracapacitor module state-of-charge (SoC) estimator based on an Extended Kalman Filter (EKF). A lumped-parameter resistive-capacitive (RC) electrical circuit representation of ultracapacitor module has been used for EKF design, wherein non-linear capacitance effects have been included through SoC-dependent capacitance term, while cell balancing effects were modeled by a second-order disturbance model. The proposed EKF-based SoC estimator has been compared to an LTI model-based Kalman filter as SoC estimator, and verified by means of computer simulations and experimentally on the dedicated ultracapacitor test setup.