The argument
The shape of these days
Fátima sits about 120 kilometres north of Lisbon on the limestone plateau above Ourém, and the practical answer is short: take the coach. Rede Expressos runs direct services from the Sete Rios terminal in Lisbon to the Fátima coach terminal in roughly an hour and a half, several times a day, and the terminal at the far end is about ten minutes on foot from the sanctuary. No car, no transfer, no planning beyond a seat.
The rail answer is the one that catches people out. There is a station named Fátima. It is Fátima-Chão de Maçãs, it is roughly 25 kilometres from the sanctuary, and its onward connections are thin. Caxarias, about 20 kilometres out, is the more useful railhead and is linked to the town by Rodoviária do Tejo on weekdays. Either way the train costs more time and money than the coach and solves nothing. If you are choosing, choose the coach or drive.
What a day trip cannot give you is the evening. The Rosary and candlelight procession at the Chapel of the Apparitions happens after dark, and the last coach back to Lisbon leaves before it. That is the honest trade. A day trip from Lisbon holds the sanctuary well: the Capelinha, the two basilicas, the tombs of the shepherd children, Mass, confession. It does not hold the procession, and it does not comfortably hold Aljustrel and the country sites where the children lived. If either of those is why you are going, stay the night.
This guide keeps to the sanctuary, because that is what one day from Lisbon actually contains. The wider Fátima landscape has its own two-day guide.
What this guide leaves out, on purpose
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Aljustrel, Valinhos, and Loca do Cabeço.
The hamlet where the children lived and the two country apparition sites lie about two kilometres south of the sanctuary on uneven ground. Fitting them around a return coach turns them into a rush, and they are the part of Fátima that least rewards one. They belong to the two-day guide.
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The evening Rosary and candlelight procession.
It takes place after dark, and coaches back to Lisbon do not wait for it. Leaving it out of a day trip is honest rather than regrettable; if the procession is why you are going, book a night in Fátima.
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Batalha, Alcobaça, and Nazaré.
Organized tours routinely bundle these with Fátima. They are worth seeing, but a day that carries four stops carries none of them properly, and Fátima becomes a photograph stop rather than a pilgrimage.