The high school event is part of Backwards Day with the girls playing football, and up until now, the boys on the sideline in full cheer attire cheering them on.
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Students upset over the decision took to social media with the hashtag #yestocrossdress to protest.
Some parents think students have the right to be angry.
"I think it is silly. They did that when I was in high school and it's all in just good fun. It's not trying to be offensive to anybody, it's just having fun," said Diane Ramirez. Her son is a senior at the high school.
Earlier on Wednesday, Chaffey's principal, George Matamala, met with parents during a monthly coffee with the principal.
Patricia Luna sat in on the meeting and says it was a tough call for Matamala to end the tradition
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"I think our principal is doing this because it's to protect certain students," Luna said.
Chaffey Joint Union High School in a statement said in part, "Our school site leaders will always err on the side of protecting our students. While this activity has been a campus tradition, we understand, too, that there are sensitivities on all sides of the issue. This is not, as it has been framed, a 'ban on cross dressing,' rather a thoughtful compromise in response to the sensitivities that have been raised by a number of students and staff. "
The powderpuff game is Friday at 7 p.m.