Background Intercostal lung herniation is a rare condition that may be congenital (20%) or acquired (80%). The isolated congenital form is exceptional, with one case reported in the literature. Case presentation We report a case of a 10-year-old French boy of Algeria origin, born with intermittent swelling of his right hemithorax. The swelling and pain gradually increased with age. A clinical examination revealed a localized swelling of his right hemithorax at the level of the midclavicular line and the fifth intercostal space. The swelling increased in size during respiratory movements and enlarged with Valsalva maneuvers. The intercostal lung hernia was treated by thoracoscopy. Conclusions This is the second case of isolated congenital intercostal pulmonary hernia reported in the French and English literature. It is the first to be treated by thoracoscopy. Based on this case we performed a review of the diagnosis and therapeutic aspect of pulmonary hernias. Electronic supplementary material The online version of this article (10.1186/s13256-019-2142-4) contains supplementary material, which is available to authorized users.