We propose a novel method to identify the transfer functions of single-input-single-output linear time invariant (SISO-LTI) dynamic systems. Our approach makes use of the operator based generalization of Prony’s method. In particular, the operator based Prony algorithm is used to reconstruct the transfer function of the system as a linear combination of rational basis functions. A considerable benefit of the proposed method is its robustness against the estimated system order. That is, if system order is over estimated, the correct system order can be found naturally. Another important benefit is that the proposed method is shown to be asymptotically robust towards zero expectation noise with the correct choice of certain evaluation functionals. The effectiveness of the proposed method is demonstrated through numerical experiments.