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In this paper, the fractional closed-loop system identification problem is addressed. Using the indirect approach, which supposes the knowledge of the controller, both coefficients and fractional orders of the process are estimated. The optimal instrumental variable method combined with a nonlinear optimization algorithm is handled to identify the fractional closed-loop transfer function. Also, two techniques are used for model selection the Akaike’s information criterion and the criterion. The performances of the proposed scheme are illustrated by a numerical example via Monte Carlo simulation and by real electronic system identification.