Meshaal, 56, entered Gaza from Egypt, through the Rafah crossing, and was greeted by armed Hamas soldiers, The New York Times reported.
He left the Israeli-occupied West Bank after the 1967 Six-Day War and had not returned to Palestinian territory since then.
Meshaal called entering Gaza his "third birth," The Jerusalem Post reported.
He said his first birth was his literal birth and the "second birth" was his survival of an Israeli assassination attempt in Jordan in 1997. His "fourth birth," he said, would come "when the whole of Palestine is liberated."
Officials said Meshaal will celebrate Hamas' anniversary Saturday.
His visit came eight days after a cease-fire between Israel and Hamas ended fighting in which more than 170 Palestinians and six Israelis died.
Hamas won a parliamentary majority in the 2006 Palestinian legislative election and forced out Fatah forces from Gaza a year later, Voice of America reported.
Meshaal is scheduled to address a rally Saturday in Gaza to discuss Hamas' strategy with Israel and reconciliation with the Fatah Party, which rules the West Bank, the BBC said.
His visit was "a fruit of the victory of the resistance over the occupation," Hamas spokesman Sami Abu Zuhri said in a statement.
Meshaal was born in the West Bank in 1956.
He moved to Kuwait after the 1967 war and later to Jordan where his involvement with Hamas began, the BBC said. He survived an assassination attempt in Jordan and was incarcerated before he was expelled and went to Qatar.
In 2004, he became Hamas' political leader in exile after Sheik Ahmed Yassin was assassinated.
Meshaal operated from Damascus, Syria, until February, when the unrest there led to another move, the BBC said. He now splits time between Qatar and Egypt.