Professor Flynn joined the Northeastern law community in 2003 after serving on the faculty of Western New England College School of Law. Prior to joining academia on a full-time basis, Professor Flynn was a staff attorney with the ACLU of Southern California. Her area of specialization, both at the ACLU and in her academic research, focuses on discrimination based on sexual orientation and gender identity.

At the ACLU, Professor Flynn litigated a wide array of issues. She argued before the California Supreme Court on behalf of three boys who had been expelled from the Boy Scouts based on their sexual orientation and religious non-belief, and she served as cocounsel in a successful Ninth Circuit challenge to the Los Angeles Police Department's practice of continuing to question criminal suspects after they had invoked their Miranda rights. In a decision thought to be the first of its kind, she secured a victory on behalf of a transgendered father who faced losing all legal rights to his child solely because of his gender identity.

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