We introduce a model system composed of two input discrete chains nonlinearly coupled to a single output chain which mimics the geometry of Y-shaped carbon nanotubes, photonic crystal wave guides, and DNA junctions. We explore the capability of the proposed system to perform logic gate operations based on the transmission of phase-shifted harmonic incoming waves. Within a tight-binding approach, we determine the exact transmission spectrum which exhibits a nonlinear induced bistability. Using a digitalization scheme of the output signal based on amplitude modulation, we show that AND, OR, and XOR logic operations can be achieved. Nonlinearity strongly favors the realization of logic operations in the regime of large wavelengths, while phase shifting is required for the OR logic gate to be realizable. A detailed analysis of the contrast ratio shows that optimal operation of the AND and OR logic gates takes place when the nonlinear response is the predominant physical property distinguishing the coupling and regular sites. These results point towards the possibility of Y-branched junctions to perform logic operations based on the transmission of traveling waves.