A fluid path structure is manufactured by way of an aligning step of aligning a first resin part with a second resin part by inserting a projection formed on the first resin part into a corresponding hole formed in the second resin part and a welding step of welding joint surfaces of the first resin part and the second resin part, thereby forming a fluid path. The aligning step is executed so as to narrow the gap between the projection and the hole to a minimum at a base side of the projection relative to a half of the height of the hole and the welding step is executed only at the base side of the projection relative to the half of the height of the hole so as to make the lateral surface of the projection only partially contact with the lateral surface of the hole.