Rede-express buses run from Lisbon to Fatima, and back every 60 or 90 minutes. They leave from the Arco Cego station - the trip takes about 90 minutes. The bus station in fatima is fairly small and... just a few minutes away from the sanctuary. I think the return trip (march 2004) was about 9 euros.
The more I think about the place the more I laugh at how people can make money out of three young children seeing the virign Mary over 80 years ago. This train will take you on a trip around Fatima (not that there is much else to see.)
If you are arriving into Lisbon by Air, you can take a bus from the Airport Bus Stop, located just outside of the Terminal approx. 100 Ft. Ask at information and they will direct you. The Bus Transportation is the best and quickest way to Fatima, besides taking a Taxi which would cost about E80. Bus is approx. (2005 price) E16. The buses are usually double decker buses and very nice. In Fatima, you can mostly walk or if yu are going to Aljustel, Valinhos or area, you can take the Little Train(bus on wheels), that goes throughout the town and area. A most enjoyable ride for both young and old.
The Fatima train station is about 25 km away from the town (Fatima). There are buses that connect the two or taxis.
The buses are not very regular so you need to coordinate your train with the bus schedule or pay he taxi which is about 16 Euros.