Open channel junctions are encountered in urban water treatment plants, irrigation and drainage canals, and natural river systems. Junctions are very important in municipal sewerage systems and river engineering. Adequate theoretical description of flow through an open channel junction is difficult because numerous variables are to be considered. Equations of junction models are based on mass and momentum or mass and energy conservation. The objective of this study is to compare two junction models for subcritical flows. In channel branches, we solve numerically the Saint-Venant hyperbolic system by combining Preissmann scheme and double sweep method. We validate our results with HEC-RAS using Nash and Sutcliffe efficiency. In junction models, equality of water stage and complete energy conservation equation from HEC-RAS are compared. Outcome of the research clearly indicates that the complete conservation energy model is more suitable in flow through junction than equality of water stage model in serious situations.