The uniforms, designed by Under Armour, will raise awareness for the Wounded Warrior Project, a nonprofit organization whose goal is to empower service members wounded in battle.
"After Under Armour presented us with the different ideas they had, we had strong thoughts on making sure the red, white and blue matched throughout, that it looked like a complete uniform head to toe," Wildcats coach Pat Fitzgerald said.
On Monday night, Northwestern apologized for any misconceptions about the uniforms.
The uniforms show what to some look like blood stains on a flag. Northwestern spokesman Paul Kennedy said Monday it's a "distressed pattern on both the stars and stripes that was inspired by the appearance of a flag that has flown proudly over a long period of time" and apologized "for any misinterpretation."
He added that Boston College used a similar design last year.
"The suggestion that these uniforms are depicting streaks of blood is completely false and uninformed," the company said as part of a statement issued Wednesday. "Under Armour will continue to support the military in the most respectful, visible and meaningful ways possible."
Northwestern gave up its purple color, but the school's "N" is on the back of the helmets and the pants.
Instead of having their names on the back of their jerseys, players will have one of the following words: duty, honor, courage, commitment, integrity, country or service.
After the game, the jerseys will be auctioned off through Northwestern, with 100 percent of the proceeds going toward the Wounded Warrior Project.
Northwestern (4-5, 0-5 Big Ten) is in the midst of a five-game losing streak. On Saturday, the Wildcats fell to Nebraska 27-24 on a 49-yard Hail Mary touchdown pass as time expired.
Information from The Associated Press was used in this report.