A hydraulic jump dissipates the excess energy of flowing water downstream of hydraulic structures, such as spillways and sluice gates. The present study investigates the effect of the submerged counterflow jet (SCJ) on hydraulic jump characteristics of stilling basins in vitro. Experiments were performed at six discharges, three cross-sections of the SCJ, and three placement distances of the SCJ from the ogee spillway toe in a rectangular flume with the length, width, and depth of 10 m, 0.3 m, and 0.45 m, respectively. A theoretical equation was first developed to obtain the hydraulic jump sequent depth with the SCJ under free jump conditions. Then, the laboratory results of sequent depths were compared with the theoretical equation values and the RMSE, MAPE, and RE values were obtained as 0.039, 7.06, and 14.9, respectively, suggesting high agreement between the data. The results indicated the SCJ had the best performance at 10–20% of the spillway discharge. The SCJ reduced the hydraulic jump’s average length and secondary depth by 32.8% and 19.6%, respectively. A method was also proposed to obtain the submergence threshold of hydraulic jump with the SCJ.