In this study, gene expression programming (GEP) was employed to develop a new equation for calculating choke flow rate as a function of fluid properties and wellhead choke characteristics. For this reason, a comprehensive databank was adopted from the petroleum industry, and then, the databank was split into three groups of training set for model construction (70% of database), test set for model evaluation (15% of database), and validation set for avoiding over‐fitting problem (15% of database). For assessing of GEP model, numerous statistical and graphical tools were applied, and then, it was compared with widely applied literature correlations. Consequently, the proposed tool in this study gives the best fit with the actual flow rate data with the average absolute relative deviation of 11.0872% and determination coefficient (R2) of 0.9695. Additionally, cumulative frequency plot demonstrates that the GEP model has the highest frequency over the database. The outcomes of the GEP model were also compared with the outputs of the artificial neural network (ANN) revealing the higher precision of the ANN than the proposed GEP model in this study. At the end, it is worthwhile that the suggested model can be used as reliable tool for choke performance modeling. © 2017 Curtin University and John Wiley & Sons, Ltd.