Flaherty is a joint associate professor of neurology and psychiatry at Harvard Medical School.

Her research focuses on voluntary control of action, and how human brains represent their bodies, two factors that help drive suffering in depression, Parkinson's, and somatoform disorders.

She has appeared on many TV and radio broadcasts as a public advocate for the abilities of patients with brain illnesses.

She was featured on the podcast The Great God of Depression, created by Pagan Kennedy, about her interactions with the writer William Styron.

[11] She was the protagonist of Bedside Manner, directed by Corinne Botz, which in 2016 won the Grand Jury Prize for Best Short Documentary, DOC NYC, Oscar-qualifying.