Naxos is the biggest and greenest of the Cyclades, with long sandy beaches, mountain villages and a busy port town; Folegandros is the opposite, a narrow, steep island with a clifftop Chora and a reputation for calm. Travellers take this crossing to go from Naxos's energy to Folegandros's quiet, usually as part of a loop through the southern islands.
It is not one of the Cyclades' busiest routes. Our route data lists two operators, Blue Star Ferries with conventional ships and Seajets with high-speed boats, and describes the service as seasonal. That makes the ferry timetable the fixed point of your plan: find a day with a sailing first, then book your rooms on Folegandros around it.
Expect the boat to call at other islands on the way. Folegandros sits between Ios, Sikinos, Santorini and Milos, and most ships reach it as one stop on a longer line. That is also why the crossing time varies with the vessel and the day.
We have less data for this direction than for most routes on our site: Ferryhopper did not have a page for it when we checked, and we did not have a sampled timetable. The figures here are from our own route data, so treat them as a guide and use the booking search on this page for the current timetable and price on your date. If there is no direct boat that day, going via Ios, Paros or Santorini is often the answer.