A system is disclosed for use in manufacturing a composite structure. The system may include a support configured to move in a plurality of directions during manufacturing of the composite structure, and a head coupled to the support. The head may have a housing that is configured to receive a liquid matrix and at least one continuous fiber and configured to discharge a tubular structure. The head may also have a nozzle operatively connected to the housing and configured to deposit a material layer onto a surface of the tubular structure as the tubular structure is discharging from the housing, and a squeegee associated with the nozzle and configured to wipe over the material layer. The head may further have a first cure enhancer operatively connected to the housing and configured to cure the liquid matrix in the tubular structure during discharge, and a second cure enhancer configured to cure the material layer deposited by the nozzle.