The protesters accused Ban of pro-Israeli bias and criticized him for failing to meet with leaders of the Hamas movement that controls Gaza. They shouted slogans and held signs criticizing him and accusing him of being biased toward Israel.
Hamas security officers beside the protesters allowed Ban's convoy to enter the territory. No one was injured in the incident.
Later, in a Gaza news conference, Ban thanked the territory's people for their "warm welcome," drawing laughter from journalists. He also said he shares the protesters' concern and frustration with what he called a "very dire economic, social and humanitarian problem" in Gaza.
Ban met with U.N. relief officials running a school and a housing project in the southern town of Khan Younis. He called for an end to violence between Israelis and Palestinians.
"All this violence must stop. Particularly I would urge that people from Gaza must stop firing rockets into the Israeli side. Indiscriminate killing of people, civilian people is not acceptable," said Ban.
Militants in Gaza launched eight rockets into southern Israel on the eve of Ban's visit. No one was injured.
Ban is on the last day of a two-day trip to Israel and the Palestinian territories
While he did not meet with Hamas officials, he met Wednesday night in theWest Bank with the head of the Palestinian Authority, Mahmoud Abbas, and urged him to continue preliminary talks with Israel.
The talks, sponsored by Jordan and the Middle East Quartet of U.N., European, Russian and U.S. mediators, are aimed at reviving the stalled Middle East peace process.
"I also note with appreciation that the Palestinians have been forthcoming in presenting counter proposals on territory and security as called for by the Quartet. I very much hope that the Israelis now will present their proposals," said Ban.
Abbas said the Palestinians were looking at other possibilities to further their cause as the talks have ended inconclusively.
He said the Palestinians had many options and would follow up on them after consulting with the Arab League. This meeting is due next week in Doha.
Palestinian leaders say the options include reviving their bid for full U.N. membership, currently on hold in the Security Council, or launching a program of civil disobedience, mass protests or a boycott of Israeli goods.
Ban met earlier Wednesday with Israeli Prime Minister Benjamin Netanyahu and urged him to help jump start the stalled peace talks by halting new settlement construction in the occupied West Bank, one of several Palestinian demands.
As he has said before, Netanyahu responded that he believes the issue should be part of the peace negotiations and urged the Palestinians to resume talks without pre-conditions.
