The FLNA gene encodes filamin A, an actin filament cross-linking protein that is ubiquitously expressed within the body. FLNA mutation causes periventricular nodular heterotopia (PVNH) and congenital heart disease. Interstitial lung disease (ILD) related to FLNA mutation has also been reported from 2011 and can be lethal. However, there are no reports of how to combine the treatment of heart disease with the conflicting treatment of lung disease. We herein report cases of two girls with FLNA mutation and both ILD and left-to-right shunts due to congenital heart disease. They presented with respiratory symptoms in early infancy and required management with long-term intubation and ventilation. However, their respiratory status improved subsequent to the closure of their left-to-right shunts even though they were small shunts with improvement in pulmonary hypertension. This suggests that early intervention with closure of cardiac shunts can prevent further deterioration of lung damage.