The Blalock-Taussig Shunt procedure is only a temporary measure in the treatment of this disorder. At 6 months of age, a repair operation is usually performed.

In most cases of pulmonary atresia without a VSD, the right ventricle is quite small and cannot function effectively as the pumping chamber that sends blue blood to the lungs. This condition falls into the category of "single ventricle" heart defects, which are discussed elsewhere. The ultimate operation for these defects is the Fontan procedure.

If the right ventricle is of normal or near normal size, then the Pulmonary Atresia Repair operation involves patching the ventricular septal defect (if present) and removing the Gore-Tex shunt that was inserted during the Blalock-Taussig Shunt procedure. Sometimes, if the pulmonary artery is of normal size, it is also necessary to remove the atretic valve and enlarge parts of the pulmonary artery through the insertion of one or more patches (see animation to left).

In more severe cases, a conduit, or tube with a valve at one end, is inserted between the branches of the pulmonary artery and the right ventricle. In essence, the closed segment of the pulmonary artery is replaced by an artificial but normally functioning pulmonary artery base and pulmonary valve.

Postoperative recovery is variable, depending on the individual's anatomy and the nature of the surgery. The average hospital stay is from one to two weeks.