El Hadary was born in Kafr El Battikh, Damietta. His father was a craftsman who owned his own workshop making furniture. El Hadary took up playing football without his parent's knowledge, washing his muddy clothes in a local river after playing in order to avoid them knowing. He was spotted by his local football team before being signed by Second Division club Damietta at age 17. In his first training session, he was offered goalkeeping gloves, having previously never worn a pair, but refused to wear them and would run the to training everyday. He made his first team debut for Damietta in 1993 at the age of 20, and after two seasons signed a pre-contract with Egyptian champions Al Ahly. In 12 years at the Cairo club he won eight Egyptian Premier League titles, four Egypt Cups, four Egyptian Super Cups, four CAF Champions League titles, three CAF Super Cups, one Arab Club Champions Cup, and two Arab Super Cups.