The event, held under the motto "Called to Freedom" was organised a day before Pope Francis and his predecessor Benedict XVI will confer sainthood on John Paul II and John XXIII in the Vatican.
Young pilgrims arrived in more than 800 buses from all across Croatia and neighbouring countries for the two-day event in the famed Adriatic town where late John Paul II held a mass during his 2003 visit.
Defying pouring rain, they walked in a procession through the old town towards the port of Gruz for an open air mass, at the same site where John Paul gave a sermon during his visit.
"We wanted to wake up young people to get to know God better, to explain to them that they are called to be free, to forgive and to love," one of the event's organisers, 24-year-old teacher Ivana Mazavac, told AFP.
Organisers said the event was the largest of its kind in Croatia.
Gatherings of young Catholics are being held in Croatia every two years in a different town since 1996.
Almost 90 percent of the 4.2 million in the European Union's newest member are Roman Catholics.
Croatia joined the EU in July.