Muhammad Idul was fishing with his parents in Buton waters off the South East Sulawesi province on Saturday when a needlefish jumped out of the water.
The fish's long slender snout sliced straight through the 16-year-old's neck and pierced the back of his skull.
The student was rushed to hospital for treatment, before undergoing risky surgery to remove the fish from his neck two days later.
'To remove the fish snout, one must be very careful because there is a large vessel in the neck, Professor Dr Syafri K. Arif told local news site Makassar Terkin.
Muhammad is recovering well but remains in hospital due to infection risks.