An attorney for Caliente Cab Company did not immediately return a call for comment.
Farmer's lawyers say the company, while denying the allegations, has agreed to pay $35,000.
They also say Caliente will add gender identity to its non-discrimination policy; amend its employee handbook with a section on customer restroom use; adopt a gender-neutral employee dress code; and train workers on the new policies.
Farmer said the incident occurred last June 24, after she attended New York City's annual Gay Pride march.