The energy balance of spatially varied flows at the junction of a rectangular open channel and a side channel is investigated by a one‐dimensional flow analysis of experimental data obtained from a laboratory channel system. By means of a large control volume enclosing the neighborhood of the junction and having the control surface located at the cross sections where the flow is unidirectional, the energy loss can be evaluated. The energy loss is then divided into two components: the boundary friction loss and the turbulent mixing loss. The turbulent mixing loss is found to be of the same order of magnitude as the boundary friction loss evaluated by Manning's formula. The loss coefficient is derived as a function of the ratio of lateral to total flow rate. An energy transfer process from the main channel flow to the lateral inflow or vice versa, which is implicit in the one‐dimensional flow analysis, can be analyzed by means of the turbulent mixing loss coefficients. The result may be applied to the calculation of energy losses in the junction or in spatially varied flows with lateral inflow in an open channel flow analysis.