Francis has begun the third leg of his trip to Southeast Asia and Oceania. He will meet with Timorese leaders and diplomats later on Monday.
He was met at the airport by the president Jose Manuel Ramos-Horta.
As the highlight of his visit, Francis will celebrate a mass on Tuesday. Some 750,000 people are expected to attend.
The last Pope to visit East Timor was John Paul II. It was in 2002.
A country under reconstruction
Francis intends with this visit to encourage the country to recover from a bloody and traumatic past.
East Timor, one of the world’s poorest countries and overwhelmingly Catholic, had been eagerly awaiting Francis’ arrival, which comes a day after the 25th anniversary of a United Nations-backed referendum that paved the way for its independence from Indonesia.
Since independence, the country has struggled to rebuild its infrastructure and economy. According to the World Bank, about 40 percent of Timorese live in poverty and half of its children suffer from stunted growth due to malnutrition.
