Flying is the most convenient way to get from Mykonos to Crete. There are no direct flights between Greek islands—all routes have a transfer in Athens—but this option is not as affected by weather or timing as ferries.
If you prefer to travel by sea, you can take a direct ferry, or if you're looking to island-hop en route to Crete, you can jump on an indirect ferry, which will stop at other islands along the way. Direct ferries from Mykonos only travel to Heraklion, the capital of Crete, so note that if you have another final destination in Crete, you will have to rent a car, arrange for a private transfer or take a bus to get there. Ferry schedules can be much more limited during the low season (mid-September through mid-June).
When planning your trip, consider this two-week itinerary, which will take you through the Cycladic islands of Mykonos and Santorini before bringing you to Crete, home of the minotaur and some of the best food in Greece.
Duration: 3 hours or longer depending on connection time in Athens
Flights between Mykonos and Crete are available year-round, so this can be a great travel option if you find yourself in Greece during the fall or winter low seasons.
There are flights from the Mykonos International Airport (JMK) to all three airports in Crete: Heraklion (HER), Chania (CHQ), and Sitia (JSH). Heraklion services the highest number of flights from Mykonos while Sitia offers the least.
These short flights only have economy seats available and can get booked up in the summer high season, so be sure to book a seat in advance if you're planning to travel at that time.
By Direct Ferry
Duration: 4.5 hours - 8 hours
If you'd like to take in the magical sights and sounds of the Aegean, consider taking a ferry from Mykonos to Crete. Fast and slow ferry options are available, which will take you directly from Mykonos to Heraklion. This is convenient if you're staying in Heraklion but even if you're not, you can easily get to your final destination by renting a car, hiring a private transfer or taking a bus.
The fast ferry is a high-speed hydrofoil, which can get quite bumpy in windy conditions, so check out slower ferry options if you're prone to sea-sickness as these vessels are larger and offer more expansive open-air deck space, where you can take in the cool sea breeze.
Economy and business class tickets are available for all ferries and you can bring a vehicle or motorbike on board, but this will increase the ticket price. It's suggested that you book a numbered seat if you take a slow ferry, or else you might find yourself struggling to find a comfortable seat on board.
By Indirect Ferry
Duration: 3.5 hours or longer depending on which island(s) you visit
If you're looking for a more leisurely way to get to Crete and want to visit other Cycladic Islands along the way, you can take an "indirect ferry" from Mykonos. These are ferries with stops at other islands, so whether you feel like popping over to Santorini for a quick lunch or want to spend a day or two on Tinos, you can do all that with this option.
Mykonos services a number of islands in the Cyclades, such as Santorini, Tinos, and Naxos, all of which offer ferries to Crete as well. Note that most of these ferry options will take you to Heraklion, so if you're staying elsewhere on Crete, you will have to rent a car, hire a private transfer or take a bus to your final destination.
Slow and fast ferries are available with this option. Note that ferry schedules become much more limited during the low season, so be sure to check that the ferries are running if you're traveling from mid-September through mid-June.