"Your policies destroyed my father's life," Yunus Emrah S., 40, shouted as he hurled a shoe at Kilicdaroglu, which missed the target.
Kilicdaroglu called the attacker a "man who has a mental problem" and told reporters he did not know the cause of the protest.
The attacker was arrested and taken to a police station for interrogation.
He reportedly arrived at the hotel where the meeting took place and asked to meet Kilicdaroglu to complain that his father did not receive personal benefits from the chemical company he used to work for after suffering a work-related injury.
The company is alleged to belong to the party's deputy chairman, Erdogan Toprak.
In April 2014, Kilicdaroglu was punched by a 28-year-old Justice and Development Party member, Orhan Ovet, an incident that was widely condemned by all political leaders.
Ovet was later expelled from the party and the opposition leader did not file a complaint against him.