Austin Lacey, 13, from California, said his classmates loved the costume and wig he chose for "Disney Day" and asked to pose for selfies with him.
But not long after arriving at school, a member of staff asked Lacey to remove the costume because it was a "distraction".
"I wore it for fun, I'm just one of those people, I like to go all out," he said in an interview with KTLA.
According to Lacey's mum Brooke Francev, the headteacher felt it was "inappropriate" for a boy to "dress like a girl".
In a Facebook post explaining the incident, Francev said her son was approached before lessons had started by a campus supervisor who instructed him to remove the costume.
"[Lacey] was informed the principal does not agree with boys dressing like girls," she wrote. "I went into the school a few hours later and met with the principal.
"He confirmed he instructed the campus supervisor to confiscate my son's costume. He reported it was a distraction and stated it was 'dangerous'. There were girls on campus in full costumes.
"The principal confirmed directly to me it was not okay for any child to dress as the opposite sex because it was too distracting.
"The statement made to me was: 'It is not okay for boys to dress like girls or girls to dress like boys'."
Francev said she was concerned with the headteacher's attitude, explaining that she'd spoken to other parents in the school who have had similar experiences.
"One boy wore a pink tutu in support of breast cancer awareness month and was nearly suspended for 'attempting to incite a riot'," she wrote.
"He was asked in front of many other students by school staff if he was homosexual and whether or not his father was involved in his life.
"This is a blatant abuse of power and I am hoping to draw as much attention to this issue as possible to prevent this from happening to other students."
A statement from Romoland School District Superintendent Dr. Julie Vitale read, according to KLTA: "This action was taken in accordance with district policies.
"At no time was there an indication that the student was expressing any particular message. The Principal's action was based upon the need to stop a general disruption to the school environment."
In response to the event and to support the LGBT community, students at Lacey's school are planning to wear clothes that break gender stereotypes, as shown by a picture Lacey's mum posted on Facebook.
"Lacey informed me the students are in an uproar over the 'Elsa dress debacle' and plan to cross dress all next week to show support for the LGBT community," Francev wrote.
"Then he showed me this flyer he and his classmates came up with and will be distributing. My heart is overflowing. I have amazing kids."
Speaking to KTLA, Francev added: "My son, personally, he’s not a transgender student but through this, he’s really taken a stand on the rights that all people have. Equal rights."