Movie is Alice in Wonderland/Wizard of Oz-like., set in modern times.
The villain Queen is a bit like Hexidecimal from ReBoot & Princess Langwidere from the Oz. books where she can change her face. I think possibly the villain didn't talk at all & just made physical gestures.
Girl is looking for her father. or brother who might have been taken by the queen through a portal into another world. I think her hair might have been black, bobbed, & fairly short. I think she wore pants or capris. (To be honest, my memory of what the protagonist looked like might be tainted by having watched Coraline).
I'm inclined to think it was an early CGI or stop motion film, but I looked up every CGI & stop motion movie made between the 80s & 2000 in any country & could not find anything that fit the description, so it could be cell animation in some unusual art style.
Possibly European, likely a dub. Seem to remember being tempted to rent it after seeing an ad for it on a very old anime tape, but I'm fairly positive the movie itself was not from Asia.
Art house vibe, probably for adults, I think it might have been too creepy & vague for children.
VHS, 90s or older. DVDs existed at the time, but I had only a VHS player.