João Álvares Fagundes (born c. 1460, Kingdom of Portugal – died 1522, Kingdom of Portugal), was an explorer and ship owner from Viana do Castelo in Northern Portugal. He organized several expeditions to Newfoundland and Nova Scotia around 1520–1521.

Fagundes, together with his second captain Pêro de Barcelos, and accompanied by colonists (mostly from the Azores and some from mainland Portugal), explored the islands of St Paul near Cape Breton, Sable Island, Penguin Island (now known as Funk Island), Burgeo, and Saint Pierre and Miquelon. He named the latter islands as the Eleven Thousand Virgins, in honor of Saint Ursula.King Manuel I of Portugal gave Fagundes exclusive rights and ownership of his discoveries on 13 March 1521.

In 1607, Samuel de Champlain identified the remains of a large cross ("an old cross, all covered with moss, and almost wholly rotted away") at what is now Advocate Harbour, Nova Scotia on the Minas Basin. Some historians have attributed the cross to Fagundes, who is presumed to have visited the spot some eight decades earlier.