Ahmad Bahar, a senior Hamas official, told the crowd that the Palestinian people "will never give up the right of return" to their homes and land in Israel.
The Gaza demonstrations on Friday came a day after similar ceremonies were held in cities across the West Bank, a sign of the continuing divisions between the two main Palestinian factions.
Hamas, which seized power in Gaza more than two years ago, reportedly prevented the Palestine Liberation Organisation (PLO) from holding Nakba events in the territory on Thursday.
The two factions have been in dispute since June 2007, when Hamas forced PLO supporters out of Gaza.
On Thursday, demonstrators marched through cities across the West Bank, holding Palestinian flags and images of Arab villages razed by Israeli forces.
In Ramallah, demonstrators waved banners reading, "The right of return is sacred," and "Return, Jerusalem And Self-Determination: Our Struggle Will Continue" as they gathered at the tomb of Yasser Arafat, the late Palestinian leader.
About 700,000 Palestinians fled or were driven out of their homes during the creation of the Israeli state six decades ago.
Palestinians demand the right for the 4.6 million descendants of those who fled in 1948 to return to their lands that are now inside Israel.