Emma Hart was the next-to-last of 17 children; her younger sister was educator and writer Almira Hart (Lincoln Phelps) (Phelps, Almira Hart Lincoln). Encouraged by her father, Emma early began to acquire an education beyond the ordinary. In 1802 she enrolled in her first school, the academy in her native Berlin, Connecticut. Her progress was so rapid that by 1804 she was teaching there, and in 1806 she had charge of the academy for a term. In 1807 she taught briefly in an academy in Westfield, Massachusetts, and then became principal of a girls' academy in Middlebury, Vermont, where in 1809 she married John Willard, a physician 28 years her senior. Her husband's nephew, a student at Middlebury College who lived in the Willards' home, gave Emma her first view of the vast difference in the educational opportunities open to men and to women. She studied her nephew's textbooks and mastered such subjects as geometry and philosophy.

In 1814 Willard opened the Middlebury Female Seminary in her home, and over the next few years she demonstrated that women could teach and girls could learn the Classical and scientific subjects commonly thought suited only to men. Her success prompted her to write An Address to the Public; Particularly to the Members of the Legislature of New-York, Proposing a Plan for Improving Female Education in 1819. The pamphlet was warmly received by such readers as Thomas Jefferson and John Adams, yet the legislators to whom the pamphlet was addressed failed to respond (several members ridiculed Willard's outline of a course of academic studies for girls as contrary to God's will), but New York Governor DeWitt Clinton invited Willard to open a school in his state.

In 1819 Willard moved to Waterford, New York, and opened a school. In 1821 she moved on to Troy, New York, where the town council had raised money to build a girls' school. The Troy Female Seminary opened in September 1821 and began its long history as one of the most influential schools in the United States. It was a pioneer in the teaching of science, mathematics, and social studies to girls, antedating Mary Lyon (Lyon, Mary)'s Mount Holyoke Female Seminary by 16 years and the first public high schools for girls (in Boston and New York City) by five years. The school attracted students from families of wealth and position and by 1831 had an enrollment of more than 300, about one-third of whom were boarding students. Willard published several textbooks, including History of the United States, or Republic of America (1828) and A System of Universal History in Perspective (1835). She also published a volume of verse titled The Fulfilment of a Promise (1831). Of her poems only "Rocked in the Cradle of the Deep" is remembered.

Willard remained head of the Troy Female Seminary until 1838, by which time hundreds of graduates—many of them teachers—had been shaped by her philosophy. Willard's later years were filled with traveling, lecturing, and writing. In 1854 she represented the United States at the World's Educational Convention in London. Among her later books are A Treatise on the Motive Powers Which Produce the Circulation of the Blood (1846), Guide to the Temple of Time; and Universal History for Schools (1849), Last Leaves of American History (1849), Astronography; or Astronomical Geography (1854), and Morals for the Young (1857). The Troy Female Seminary was renamed the Emma Willard School in 1895.