This question comes up on every Greece travel forum and it generates strong opinions. People who loved Santorini defend it fiercely. People who loved Mykonos do the same. And there is always someone who says neither, go to Naxos instead, which is good advice but does not answer the actual question being asked.
I have spent time on both. Here is an honest comparison based on what the islands actually deliver, not what the travel industry says they deliver.
Santorini: The View Is Real, the Experience Is Complicated
The caldera view from Oia is one of the most beautiful things in Europe. The white and blue buildings cascading down the volcanic cliffs to the dark water of the flooded crater, with the shadow of the opposite cliff and the distant silhouette of Thirasia across the water: it is everything the photographs promise. The problem is that between thirty and forty thousand tourists arrive on the island every single day in summer, most of them trying to stand in the same spot to photograph it.
The southern part of the island around Akrotiri and the red beach is significantly less crowded. The ancient Minoan city buried under volcanic ash at Akrotiri is genuinely one of the most extraordinary archaeological sites in the world and receives a fraction of the attention of the caldera viewpoints. If you visit Santorini for the archaeology and the wine rather than the Instagram, it delivers at a completely different level.
Mykonos: Party Island With a Prettier Old Town Than You Expect
Mykonos has a reputation as an expensive party destination that puts off travellers who are not coming for that specific reason. The reputation is earned: the beach clubs are real, the prices are genuinely high, and the volume of nightlife in July and August makes sleep difficult in most of the island’s accommodation.
What the reputation obscures is that Mykonos Town, the old part of the island, is one of the most beautiful small towns in Greece. The Chora neighbourhood with its whitewashed labyrinthine lanes, the windmills above Little Venice, and the pelicans that wander around the harbour like local celebrities: none of this has anything to do with the beach club scene and all of it is worth seeing. Go in May or October and you get the beauty without the noise.
The Verdict: Which Should You Choose?
Choose Santorini if you are coming for the landscape and the archaeology and you book accommodation well off the main tourist drag in a village like Pyrgos or Megalochori rather than Oia. Choose Mykonos if you want a base for island-hopping to Delos and Naxos and you visit outside July and August.
Choose neither if you are on a tight budget: both islands charge significantly more than the rest of Greece for accommodation, food, and activities. The Cyclades have dozens of islands that offer a comparable quality of scenery and a fraction of the prices. Paros, Naxos, and Milos all do versions of what Santorini and Mykonos offer without the infrastructure that makes those islands feel like a theme park version of Greece at peak season.
When to Go: The Same Answer for Both
May and early June, or September and October. The weather is warm, the sea is swimmable by late May, and the crowds are a fraction of what they are in July and August. Prices for accommodation on both islands drop by thirty to fifty percent outside peak season. The islands are genuinely better in the shoulder months and not just cheaper.