There are normally 3 ferries a week to Koufonisia from Piraeus, the main port of Athens.

Except from Piraeus port, there are also ferries to Koufonisia from:
Athens, Rafina – Amorgos, Aegiali – Amorgos, Katapola – Donoussa – Folegandros – Ios – Iraklia – Milos – Mykonos – Naxos – Paros – Santorini (Thira) – Schinoussa – Sifnos – Syros. Note that these ferry connections can be available only during some summer months.

A ferry to Koufonisia also runs all year round from Naxos and Amorgos.

The most popular ferry routes to Koufonisia are from the ports of Naxos, Piraeus (Athens), Mykonos, Santorini, Amorgos (Katapola) and Paros. Note that Mykonos, Santorini and Paros have an international airport and Naxos has a national airport with flights from Athens. Visitors can get there by plane and then reach Koufonisia by ferry.

From Naxos the ferry roughly takes about 2 to 2.5 hours (except Sundays) to Koufonissia with the Blue Star Ferries and the Express Skopelitis. The Blue Star ferries sail 3 x a week from Naxos to Koufonissia. Express Skopelitis sails daily and in peak season the Sea Jets and the Hellenic Seaways takes around 40-50 minutes. There are catamarans sailing 7 times a week during peak season and it takes around 35 minutes.