Portuguese President Jorge Sampaio and his wife Maria Jose Ritta greeted the pope as he stepped out of the Alitalia plane at Lisbon's military airport shortly after 6 p.m. local time. Prime minister Antonio Guterres and Portuguese church officials were also at the aiport.
The pontiff, who turns 80 next week, then went by helicopter to Fatima, 110 kilometers (70 miles) north of Lisbon.
The beatification ceremony is scheduled for Saturday morning at the sanctuary.
Tens of thousands of people of many nationalities have streamed into the rural town, many of them exhausted pilgrims who walked for days and slept in the open air.
Three shepherd children said the Virgin Mary appeared to them six times at Fatima in 1917.
Jacinta Marto and her brother Francisco, the two children to be beatified, died when they were nine and 11 years old. The surviving child, their cousin Lucia de Jesus dos Santos, now 92, has been at a Carmelite convent in central Portugal since 1929. She will meet the Pope on Saturday.