Reed is arguing that the provision where insurance companies must provide coverage for contraceptives and abortion-inducing pills is unconstitutional.
Reed is a devout Christian and feels the law is hindering his freedom of religion.
"There has to be a point where the government can't tell us that we have to violate our morality in order to be legal," Reed said.
Reed is not the only company to challenge the law.
The University of Notre Dame and Hobby Lobby have filed lawsuits fighting the law.
President Obama said that it's not going anywhere in a speech on Thursday.
"We're not repealing it as long as I'm president," Obama said.
Reed's court filing lists Plan B and Ella as specific contraceptives that his company would have to provide to his 179 full-time employees.
Supporters of the Affordable Care Act say it would not be fair to pick and choose what benefits company's cover.
The Supreme Court is expected to rule on the case sometime next year, leaving Reed and other businesses waiting and wondering what will happen next.