Ratramnus of Corbie, a ninth-century Frankish monk, wrote a letter on cynocephali ("dog-headed men"), in which he discusses whether the dog-headed men who live at the ends of the earth were capable of salvation.

Ratramnus notes that cynocephali live in towns and grow crops, and display reason - which seems to fit your description. He seems fairly comfortable with the idea that cynocephali exist, although he doesn't claim to have met them himself.

The letter is translated in Paul Dutton's "Carolingian Civilisation: a reader" (1993) [EDIT - I thought it was, but I just flicked through my copy and couldn't find it there - sorry.]

Ibn taymiyya a 13th century Muslim theologian believed that God was constantly creating. This includes the creation of sentient species. Jon Hoover published an article about it. Title is something like constancy of creation in the thought of ibn taymiyya. This might include the modern idea of aliens or extra terrestrials.

Sorry on my phone or I would find a link.

Are you asking only about extraterrestrials, or including things from earth people ascribed human level intelligence to, like say certain animals? If the latter, the Japanese often told tales of various animals, in particular foxes and raccoon dogs, who had human like behavior and motivations. Though to what extent they were considered "non-supernatural" is debatable.

"The Middle Ages inherited from the Greeks that beyond the boundaries of the world there lived types of humans very different from us. They might be gigantic, they might be pygmies. Some had faces in their chests, others only one eye. They could be threatening, like the cannibals, or appealing, like the people who had no mouths and survived by smelling fruits and flowers."

-Robert Bartlett, The Natural and the Supernatural in the Middle Ages.

The citation for the paragraph is "The Monstrous Races in Medieval Art and Thought", by John B. Friedman. Bartlett then goes on to discuss the dog-headed men mentioned by AbpStigand, as well monopods, people with a single massive foot that like to lie down and use it as an umbrella.

In another book, England Under the Norman and Angevin Kings, Bartlett discusses a variety of other strange creatures that might fit what you're looking for.

There were legends of the Portuni, "diminutive beings with wizened faces who wear tiny clothes." There was a report of an underground kingdom of what would be perfectly normal humans, except for their green skin. Finally, there was another report of "aerial mariner(s)", who sailed through the sky, and would suffocate in our lower atmosphere the same way humans drown underwater.

Interesting question, thanks for the prompt to revisit some of my favorite history books!