"Women's career trajectories are blunted because they are marginalized and passed over for promotions. Nike judges women more harshly than men, which means lower salaries, smaller bonuses, and fewer stock options," the lawsuit reads. "Women's complaints to human resources about discrimination and harassment, including sexual assault, are ignored or mishandled."

The complaint, which seeks class-action status, is led by former employees Kelly Cahill and Sara Johnston, who worked at the company's Beaverton, Oregon, headquarters. Cahill now works for rival Adidas.

The suit filed Thursday in U.S. District Court in Portland, Oregon, says the sports apparel maker "intentionally and willfully discriminated against [women] with respect to pay, promotions, and conditions of employment."

A group of female former employees of Nike are suing the company over allegations that it systematically discriminated against women and fostered a hostile work environment, according to a lawsuit.

In a statement to CNBC, Nike said they oppose discrimination in any form. "We are committed to competitive pay and benefits for our employees. The vast majority of Nike employees live by our values of dignity and respect for others," the company said in the statement.

Complaints first surfaced at Nike in March when a group of women presented CEO Mark Parker with a survey on gender discrimination.

Nike reacted swiftly with Parker quickly restructuring his leadership team and announcing that then-President Trevor Edwards would retire in August.

Edwards, who was being groomed to be a possible successor to Parker, has been blamed in the lawsuit for creating and exacerbating a "hostile work environment."

The company also admitted it failed in hiring and promoting women, ousted at least 11 executives and announced raises for 7,000 employees after conducting an internal review of its pay practices.

The CEO apologized to employees in May.

"We, and I, missed something. While many of us feel like we're treated with respect at Nike, that wasn't the case in all teams. And if all of our teammates don't see the same opportunities, we just can't accept that," he said at the time.

In the lawsuit, Cahill cites a culture where women felt excluded, were subject to hostility and were referred to in demeaning ways. She resigned from Nike in 2013. Cahill says she voiced her complaints to human resources at least four times to no avail.

"For many women at Nike, the company hierarchy is an unclimbable pyramid - the more senior the job title, the smaller the percentage of women," the suit reads. "Women's career trajectories are impacted because they are marginalized and passed over for promotions."

The group is seeking changes in company pay practices, a court-appointed monitor, back pay and an unspecified amount of punitive damages.

"The way Nike marginalizes women at its headquarters is completely contrary to how it portrays itself to its customers as valuing women in sports and the importance of providing equal opportunity to play," said Byron Goldstein of Goldstein, Borgen, Dardarian & Ho, which is representing the women.

Meanwhile, Nike's stock has not seen any material impact. The shares are trading near its all-time highs.

— CNBC's Nick Wells contributed to this article.