Perez Trabelsi, head of the Tunisian Jewish community, said he was comforted to know that there was a heavy police and military presence on Djerba, which is 500 kilometres from Tunis.
"Everything is going properly. I am satisfied," he said. The pilgrimage involves many traditions, including lighting candles at the synagogue, the giving of rabbinic blessings and a procession through Djerba.
Ten years ago, Tunisian Jewish life was shattered when an al-Qaeda suicide bomber drove a truck loaded with explosives into the synagogue's outer wall. More than 20 people died in the attack, which came just days before the festivities.
But last month Tunisian President Moncef Marzouki took part in a commemoration of the attack, a move which was observed with cautious optimism by the Jewish community.
The Tunisian Jewish community dates back two millennia. Before the North African country gained independence from France in the 1950s the population stood at 100,000.