Thomas explained that she is Native American and that she has been sitting out the Pledge of Allegiance as a peaceful protest to the way Native Americans have been historically treated in the U.S.
"My dad and my mom brought up what [the pledge] meant to us and our people and what happened -- you know, the history," she said. “So I just started sitting down.”
Thomas added that she had never had a problem until recently, when her advisory period teacher at Lower Lake High School in Lower Lake, California, lowered her and a classmate's participation grades.
The teacher "told me I was being disrespectful," Thomas told KXTV. "I was pretty mad because she was being disrespectful to me also, saying I was making bad choices and I don’t have the choice to sit down during the pledge."
This past week, the issue came to the attention of Konocti Unified School District Superintendent Donna Becnel, who confirmed the incident took place.
"One of the students let a principal know what happened and the principal then informed me," Becnel told ABC News today. "We've since transferred the two students to another [advisory period] class."
The superintendent said she stands behind the students and their right to free speech.
"Students here have First Amendment rights, and they do not lose that when they come to school," Becnel explained. "If any students have any concerns about their right to free speech, they can speak with a site administrator. We also have policies in place to protect their right."
And while Becnel said she took the "unfortunate incident" seriously, she also hoped it "does not overshadow the great work that the rest of the district's staff and teachers have been doing."
Becnel added that the teacher who lowered the students' participation grades had only started working for the district this school year and that the district has never had any First Amendment issues in the past.
Bencel said she could not divulge what consequences, if any, the teacher could face, explaining that personnel matters were confidential.
ABC News was not immediately successful in reaching Thomas or her parents for additional comment today.