The flyers featured the phrases "save the baby seals" and "save the baby whales" crossed out, with "save the baby humans, stop abortion" written underneath.
Nicholas Zinos, whose daughter is a sixth-grader at Nova Classical Academy, filed the lawsuit Friday, the St. Paul Pioneer Press reported.
The lawsuit stated Zinos' daughter brought anti-abortion flyers to hand out to her classmates in February. The school, however, did not allow her to pass them out, the suit alleges.
In a letter to Zinos included in the court filing, Nova Classical Academy said the school limits political, religious and controversial speech to its high school students in response to parental concerns.
"There are places for students to express their thoughts and opinions, whatever they are ... but not everywhere and anytime within the walls of a school," Nova Executive Director Brian Bloomfield wrote in the letter.
The lawsuit alleges the policy gives administrators "unbridled discretion" to limit student speech, violating their First Amendment rights.
"Unless there is a material disruption, students have the absolute right to distribute materials at school," said Matt Sharp, an attorney with the Alliance Defending Freedom, an Arizona-based legal advocacy organization representing Zinos. "There was no evidence of disruption at the school at all."
The school has not yet commented on the lawsuit.