A day trip from Lagos to Fatima makes a very long day.
There is no easy train connection as Fatima station is 20km from Fatima with infrequent bus connections.
There is effectively only two ways to currently make the trip:
Viamichelin.pt gives a distance of 381km one way with a transit time of 4hrs 15minutes, so +- 800km return trip by toll motorway.
Based on February 2015 prices, the estimated cost by car would be:
Tolls: One way 31.35 €
Fuel (based on prevailing prices): 43.62 €
By public transport, one would have to use the long distance EVA TRANSPORTES/REDE EXPRESSOS bus service via Lisbon Sete Rios Bus Station.
See the Rede Expressos website: http://www.rede-expressos.pt/
A day return trip only really works on weekdays. If one catches the 05:45 EVA departure (Monday to Friday) from Lagos Bus Station, one arrives in Fatima at 11:30. There is a 60 minute layover in Lisbon.
One can then get the 18:30 departure back from Fatima, arriving Lagos at 00:15. Again there is a layover in Lisbon.
These are both daily services and times are correct as of February 2015.
As far as the writer is aware, there are currently no organised day-trips from Lagos to Fatima.
One can contact the information services at the Sanctuary for more information about the Sanctuary:
By Aracuano (Own work) [GFDL or CC BY-SA 3.0], via Wikimedia Commons