Ghannouchi's British Airways flight to Tunis was due to depart at 08:30 GMT and arrive at 11:25 GMT, AFP reported.
Ghannouchi checked in at Gatwick accompanied by 30 supporters and journalists to return to Tunisia after 22 years in exile in Britain.
"I feel very happy today," he said. "I am still the leader of my party. I want to organize a conference."
"If there are free and fair elections Ennahda will take part -- in the legislative elections, not the presidential elections," Ghannouchi added.
"There is still confusion regarding the political situation," he went on to say. "The interim government is changing its ministers every day, it's not stable yet and its powers are not clear yet."
"It's not clear who it is accountable to because the current parliament is still the one-party parliament," he concluded.
His return comes after Tunisia's interim government issued an amnesty for all the country's banned political activists. The amnesty is yet to be approved by the parliament.
Ghannouchi, who left Tunisia shortly after Ben Ali came to power in a 1987 coup, is not expecting to return "triumphantly" and wants to return simply as "a free man," AFP quoted his spokesmen as saying.
The 69-year-old leader earlier said that he plans to let younger people take over his once outlawed Ennahda (Awakening) movement.
Meanwhile, the new government installed after Ben Ali's fall has unveiled unprecedented democratic freedoms, including lifting media restrictions, releasing political prisoners and registering banned parties.
Ghannouchi also emphasized that he does not plan to run for president, but he wants to turn his movement into a political party that will take part in the country's first democratic elections.
Ben Ali and his family fled to Saudi Arabia on January 14 after days of street protests put an end to his 23-year rule.
Thousands of protesters have kept up their daily rallies in the streets of the Tunisian capital, Tunis, calling for old regime politicians to be swept from power and for the abolition of Ben Ali's Constitutional Democratic Rally party.
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