The five-year-old boy was staying at a refugee centre near Warsaw after arriving in Poland with his family on August 23. But a day later he was taken to hospital after eating the poisonous mushrooms with his six-year-old brother, who is critically ill.
The hospital’s director, Dr Marek Migdal, on Thursday confirmed the death of the five-year-old.
He said: “Unfortunately, we were unable to help both boys.”
The five-year-old had suffered irreversible brain damage and was not able to have a liver transplant like his older brother.
A 17-year-old Afghan girl was also admitted to hospital after eating mushrooms at the refugee centre.
The young brothers and their family were evacuated from Kabul by the Polish military following the Taliban takeover of the country.
The Taliban swept to power last month amid the withdrawal of foreign forces.
The evacuation effort came to a close on Monday as the last US troops left Afghanistan.