In irrigation and drainage structures, side weir is widely used for flow diversion from main to branch channels. Side weir is also used as a measuring device for discharge measurements, so discharge coefficient was mainly studied in many previous studies. Skew side weir was not taking a good highlight in previous studies and literature, so the present work discharge coefficient calculation for the skew side weir was adopted and studied. Multiple Linear Regression (MLR) and Gene Expression Programming (GEP) tools were used in the present study and compared with observed values of C d. The mean absolute error for C d observed and calculated in MLR and GEP was not exceeded 5%. The C d values for skew side weir ranged from (0.65) to (0.85), while its values for straight vertical side from previous literature weir ranged from (0.45) to (0.65); this mean skew side weir can be used for increase in discharge diversion to the branch channel at the same water levels by 27%. The Akaike information criteria (AIC) with (AICs), root-mean-square error (RMSE), mean absolute relative error (MARE) and scatter index (SI) are used in this study for measuring the GEP model performance. From results, the GEP model has AIC = − 216.51, AICs = − 918.51, RMSE = 0.004653, MARE = 0.005234, R 2 = 0.994 and SI = 0.006231 performed the best. According to previous results, the new equation presented through GEP can be adopted for discharge coefficient calculation in skew side weir.