At one point, a guidance counselor suggested that the student switch out of a journalism class whose teacher had insisted she stand, according to the lawsuit. This year, a teacher told the teenager’s class that those who sat through the pledge were comparable to Soviet communists, pedophiles and Islamist extremists, the lawsuit said. Classmates harassed the teenager online and in person, including as recently as last week, Mr. Kallinen said.

Because of the harassment, Ms. Arceneaux decided in the spring to home-school her daughter before allowing her to return to school in August, according to the suit. The teenager, who said on Wednesday that she had a 3.9 G.P.A., continued to participate in debate competitions while being home-schooled, but at an expense of more than $10,000 to the family, according to the suit.

In a statement, the Klein Independent School District disputed the accusations.

“Klein I.S.D. denies the allegations and, after investigation and discussion with those involved over a three-year span, finds multiple discrepancies in the allegations,” the statement said. The district added that it respected the rights of its students and “does not tolerate harassment” against them.

Ms. Arceneaux said her daughter made the decision to protest the pledge on her own, but added that she understood the reasoning.

“Obviously in this country I can see there’s not liberty and justice for all,” Ms. Arceneaux said at the news conference. “I’m still an African-American woman in this country, and I can see the news and things that go on around me.”

The lawsuit is funded by American Atheists, a nonprofit that fights for the separation of church and state and has helped students with similar disputes. It joined the effort after Ms. Arceneaux and her daughter reached out, a spokesman said. Neither the teenager nor her mother is an atheist, Mr. Kallinen said.