A method for manufacturing a manifold for a fuel cell with a multilayer structure by injection-molding individual manifolds, each having welding projections and welding guides, and bonding the injection-molded individual manifolds by vibration welding includes arranging welding projections of an upper individual manifold and welding guides of a lower individual manifold to be engaged with each other while maintaining a uniform gap between each other to bond a plurality of individual manifolds in an up and down stacking structure, pressing the lower individual manifold upward, and applying vibration to the upper individual manifold in the left and right direction, thus bonding the upper and lower individual manifolds. Among the welding projections of the upper individual manifold, a non-horizontal welding projection whose longitudinal direction does not coincide with the vibration direction of the individual manifold has a variable height.