This study aimed to use the response surface (RS) method for finite element (FE) model updating, using operational modal analysis (OMA). The RS method was utilized to achieve better agreement between the numerical and field-measured structure response. The OMA technique for the field study was utilized to obtain modal parameters of the selected historic masonry minaret. The natural frequencies and mode shapes were experimentally determined by the enhanced frequency domain decomposition (EFDD) method. The optimum results between the experimental and numerical analyses were found by using the optimization method. The central composite design was used to construct the design of experiments, and the genetic aggregation approach was performed to generate the RS models. After obtaining the RS models, an attempt was made to converge the natural frequency values corresponding to the five-mode shapes with the frequency values identified by the experimental analysis. ANSYS software was used to perform 3D finite element (FE) modeling of the historic masonry minaret and to numerically identify the natural frequencies and mode shapes of the minaret. The results of the experimental, initial, and updated FE model were compared with each other. Significant differences can be seen when comparing the experimental and analytical results with the initial conditions.