If you're writing in third person, this will be a snap. Using “he" or “she" to refer to your character will be a quick give away. If you're not using third person, there may be opportunities for other characters to refer to the character in third person: “She's driving me crazy." Also, a gender specific name can make this information clear from the get go.
What's probably more important, however, is making sure you fully characterize and accurately portray how this character inhabits his or her identity. If she's not very girly, she's bound to feel a bit out of place changing after gym near her high school's super glamorous cheerleading squad in the locker room. Or, you can focus on where she does feel comfortable. It may be on the wrestling mat, or at the telemarketing company where she works after school, or just hanging out with her family watching late night television before bed. How your character behaves and thinks will reveal her essential nature.
Keep in mind: not all females are ruffles and lipstick and pink. Not all males are rugged and entranced by football. And those who do fit the stereotype of their gender have other interests and inclinations, too. By staying away from gender stereotypes, you're working toward more multidimensional characters. So, don't worry too much about gender-specific traits. Just reveal your character honestly and fully and the reader will understand her or him in all of her or his individuality.