She began Christian Science healing in Boston, and in 1885 led the service on alternate Sundays at Chickering Hall. The next year she was sent by Eddy to New York, where she organized the First Church of Christ, Scientist in 1887. She was appointed pastor of that church in 1888, and in 1895 was made first reader when the title of pastor was changed in all Christian Science churches. For a time she was also principal of the New York City Christian Science Institute (chartered 1878).
In the early 1900s Stetson raised more than $1,250,000 to build a structure for the use of First Church, on West 96th Street at Central Park West, which was dedicated free of debt. In 1909 she was excommunicated by the Mother Church at Boston, on charges of insubordination and of false teaching.