Francisco Alvarez (1465?-1541?) was a Portuguese missionary and explorer.

Born in Coimbra, Portugal, as an adult he was a chaplain-priest and almoner to King Manuel I of Portugal. He was sent in 1515 as secretary to Duarte Galvão and Rodrigo de Lima on an embassy to the negus of Abyssinia (modern-day Ethiopia). The expedition having been delayed on the way, it was not until 1520 that he reached his destination. He remained six years, returning to Lisbon in 1526-1527.

In 1533 he was sent to Rome on an embassy to Pope Clement VII. The precise date of his death, like that of his birth, is unknown, but it must have been later than 1540, in which year he published at Lisbon under the king's patronage an account of his travels in one volume folio, entitled Verdadeira informação das terras do preste João das Indias ("A True Relation of the Lands of Prester John of the Indies"). The information it contains must, however, be received with caution, as the author is prone to exaggerate, and does not confine himself to what came within his own observation.

Alvarez's work has been translated into English a number of times. A recent translation is by C.F. Beckingham and G.W.B. Huntingford, The Prester John of the Indies (Cambridge: Hakluyt Society, 1961).