There's no standard size for a middle school gym. The size varies greatly depending on the school's budget, the size of the school, and the local building codes. You could find gyms that are relatively small, suitable for only one basketball court, or much larger ones capable of accommodating multiple courts and other activities.
A reasonable estimate might range from approximately 6,000 to 12,000 square feet, but this is just a broad guess. Some will be smaller, some significantly larger.