The two feel different. Lourdes is a town in the foothills of the Pyrenees, and the sanctuary lies along a river: the Grotto of Massabielle, the spring, the baths, and the basilicas built above them. Sick and disabled pilgrims have the first place there, accompanied by volunteers, and that sight is what most people remember. Fátima is an open plateau in central Portugal. Its heart is the small Chapel of the Apparitions on a vast esplanade, and the village of Aljustrel, where the children lived, is about 2 km (a little over a mile) away on foot. Fátima is plainer and quieter on ordinary days, and immense on the 12th and 13th of each month from May to October.
Practically, Fátima is about 130 km (80 miles) north of Lisbon and is usually reached by road. Lourdes has its own railway station, with direct TGV trains from Paris, and small airports nearby. Fátima’s candlelight procession follows the evening Rosary every night of the year, weather permitting; at Lourdes the torchlight procession is held each evening during the pilgrimage season, roughly April through October. Both sanctuaries are level and manageable for wheelchairs.
If you cannot decide, you do not have to: the two fit in one journey of nine or ten days. They are about 900 km (560 miles) apart with no direct train, so plan a full travel day between them. If you can only go to one, let the story decide. Lourdes is for those who want to pray for healing or to serve the sick; Fátima is for those who want to pray the Rosary where the children did.