CHICAGO — An intelligence analyst for the FBI in Chicago who allegedly missed becoming a special agent by a single pushup has filed a gender-discrimination lawsuit alleging that the FBI’s fitness test is flawed and biased against men.

Jay Bauer, a Northwestern University doctoral graduate, joined the FBI in 2009 after leaving the University of Wisconsin at Milwaukee as an assistant professor in its communication sciences department, according to the lawsuit filed last week in federal court in Chicago.

Bauer passed a fitness test before entering new-agent training at Quantico, Va., where he scored at or near the top of his class in everything from firearms training to academics, according to his lawsuit. He was also selected by his fellow trainees to be their class leader, the lawsuit said.

Trainees must pass another fitness exam at the FBI Academy. Men must complete at least 38 situps in a minute and do 30 untimed pushups. Male candidates also must sprint 300 meters in 52.4 seconds and run 1.5 miles in 12 minutes and 24 seconds.

Bauer allegedly fulfilled all the other requirements, but after managing to do only 29 pushups, he was forced to resign from special agent training, the lawsuit said. He took an FBI analyst’s job in Chicago, where he’d already relocated his wife and two young children. He lives in Mount Prospect.

For the past two years, Bauer has challenged the FBI decision through the administrative courts.

His attorneys argued that a female trainee who scored near the bottom of the class in firearms proficiency was given another attempt at the fitness test, but Bauer wasn’t.

They also argued that the FBI’s fitness standards — which before 2003 required men to do just 25 pushups — are comparatively harder for males. Female trainees must complete at least 14 untimed pushups, an amount equal to between 27 and 29 for men, the lawsuit says, citing a database maintained by a fitness consultant the FBI worked with in drafting the guidelines.

His attorney said in a letter filed to the administrative law judge that Bauer didn’t want to take the legal fight to federal court — he was being considered for promotion in his current job — and instead sought a settlement conference with the FBI.

“Given what is occurring in this world today and the fact this case is about one pushup, it does not feel right (to file a lawsuit),” his attorney Michelle Reese Andrew wrote to an administrative judge.

But Bauer, feeling that he wasn’t being given a fair hearing in administrative court, filed his challenge last week in federal court, asking that he be put in a special agent position with back pay and that the Justice Department be ordered to pay his attorneys’ fees and damages.

“My client is a reluctant plaintiff,” Andrew said in a brief telephone interview. “He feels compelled to fight for what’s right here.”

An FBI spokeswoman said the agency doesn’t typically comment on pending litigation.