The U.S. Supreme Court ruled in Price Waterhouse v. Hopkins that sex discrimination under Title VII applies to gender stereotypes. It only makes sense that Title IX would follow the same guidelines.
"Five federal appeals courts have explicitly ruled that transgender people are protected against discrimination under federal laws prohibiting sex discrimination, as have dozens of federal district courts and state courts. When transgender people face discrimination because they don't conform to employers' expectations about how men and women should look, behave, or identify, that's sex discrimination."
Price Waterhouse v. Hopkins