Technically, yes. But you could argue that a "Marvel movie" has become something else in the intervening decades -- something less about studio ownership (Marvel is owned by Disney now, anyway) and more about a devotion to superheroes saving/destroying the world two or three times per year.
In that sense, 1986's "My Little Pony: The Movie" is not a Marvel movie. The stakes are markedly lower -- the plot revolves around a mean witch trying to spoil the ponies' spring festival, rather than, to take one notable "Marvel movie" example, a power-mad immortal being wiping out half of all life in the universe.
But, yes, in the production-ownership sense, "My Little Pony: The Movie" is a Marvel movie. In fact, in the '80s the comic book company's movie arm was spending more time on toy-based movies than comic-based movies. Its next few productions included Transformers and G.I. Joe features (as well as a second My Little Pony flick).
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