The overland option can make sense for a group that wants intermediate stops in northern Spain as part of the purpose. Treat the connection as its own itinerary decision and budget a full day for it either way.
Fátima · YOUR QUESTION, ANSWERED
How do I get from Fátima to Lourdes?
Fly, in most cases. The shrines are roughly 900 km apart with no direct train, so the practical choices are a 9 to 10 hour coach day overland or a flight day via Lisbon or Porto with a connection to Tarbes-Lourdes-Pyrénées (about 10 km from Lourdes), Pau (about 45 km), or Toulouse (about 180 km, 2 hours by road). Compare real flight connections and ground transfers for your dates, or accept that an overland route requires substantial travel time.
Sources & further readingShrine of Fátima: official siteSanctuary of Lourdes: official site
Official sources cover institutional information. Suggested pacing and itinerary choices are planning guidance. Check current arrangements for your travel dates.