My Highlander has been making this terribly loud noise every time I hit the brakes. I think it might be mechanical stress on the brake system but I'm not sure.

What kind of noise? When was the last time you had the brakes serviced? Is it coming from the rear, front or both?

Hey, it could be that your brakes pads are worn down. They will squeal when they need to be replaced. If you have a mechanic you trust, he should be able to tell you just by looking at it whether this is the case, without even touching your car. Also, it could just be that they're really dirty.
To clean them, I think they do have to be taken off, but at least they don't have to be replaced if that's it.