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This paper deals with continuous-time system identification using fractional models in a noisy input/output context. The third-order cumulants based least squares method (tocls) is extended here to fractional models. The derivatives of the third-order cumulants are computed using a new fractional state variable filter. A numerical example is used to demonstrate the performance of the proposed method called ftocls (fractional third-order cumulants based least squares). The effect of the signal-to-noise ratio and the hyperparameter is studied.