She began her teaching career in Chestertown, Maryland, but was hired by the Cambridge School Department in 1882 (after some pressure from the local African-American community).

She was a teacher at the Agassiz until her appointment as principal in 1889. In 1916, when she was made master, she became one of two women in the Cambridge school system and the only African-American in New England to hold such a position.

To keep up with her field she took courses at Harvard and other institutions, and she in turn taught in the summer normal courses for teachers held at Hampton Institute in Virginia and the Institute for Colored Youth in Cheyney, PA.

She organized the first Parent-Teacher group in the Cambridge Public Schools, introduced new methods of teaching mathematics, began art classes, and inspired the beginning of a museum of science program within the school system.

Under her leadership, the Agassiz became the only public school in Cambridge (and perhaps anywhere in the US) to establish an "open-air" classroom (then thought to be good for frailty and pulmonary ills and wise measure for healthy children as well). She was also the first to introduce the practice of hiring a school nurse.

Baldwin's concern for children's well-being is legendary and she was an inspiration to generations of students, parents, educators and community members, not just in the public schools, but beyond.

Upon her death in 1922, Baldwin was greatly mourned. Her friends, pupils and colleagues at the school established a scholarship for Agassiz pupils and named the school's auditorium in her memory.