The Pope took off from Rome's Fiumicino Airport shortly before 9am on Thursday morning and his Alitalia flight landed shortly after 10am.
His plane was met by former members of the Swiss guard and by Swiss President Alain Berset as well as other members of the Swiss government ministers.
"This is a trip towards unity," the pontiff told reporters on the plane before landing, according to the AFP news agency.
The 81-year-old is coming to Geneva on the invitation of the World Council of Churches (WCC) which has some 350 member churches and represents around 500 million Christians globally.
The Roman Catholic Church is not a member of the WCC but it does send observers to WCC meetings.
The Pope's attendance at the event has been seen as highly significant in terms of bridging the divide between the Vatican and other Christian churches.
Pope Francis will also hold a mass at Geneva's Palexpo convention centre at 5.30pm. Palexpo said the event was full, with 41,000 people having registered their attention to come to the mass – the vast majority of them from French-speaking Switzerland.
Extra trains have been put on for people coming to Geneva for the mass while pilgrims began arriving many hours before the event itself.
Geneva Airport has warned travellers to arrive at the facility at least three hours before flights and asked members of the public only to come to the airport if absolutely necessary. Air traffic over the city will be restricted.
Police in the city have asked people to use public transport because of changed road conditions during the Pope's visit.
Around 200 soldiers with the Swiss army have been called to assist cantonal police in Geneva with security.