Francis Joseph Nicholas Neef was born in 1770 in Alsace, France. He served in the French Army when Napoleon was a rising young artillery officer. In 1796, Neef received a serious head wound and, while recovering, read the works of the great educator Johann Heinrich Pestalozzi. Upon recovery, he applied for a position at Pestalozzi's school in Switzerland, and in 1800, joined the facility to teach foreign language. Pestalozzi headed a greatly admired school where students were responsible for their own discipline, and democracy was the order of the day. William Maclure thought that Pestalozzi's school was the most rational system of education he had ever seen. Robert Owen had followed the system in setting up his school for the New Lanark Mill children.

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In 1803, Neef married Luise Buss, by proxy, because Neef was in Paris at the time and Miss Buss, as an unmarried woman, was not allowed to travel alone.

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In 1806, Maclure persuaded Neef to open a similar school in Philadelphia, Pennsylvania. When Neef came to America he modified the Pestalozzian method of education. He believed in education for all levels, not just for the poor. Neef questioned the theory of educating according to class; in America, especially on the frontier, class distinctions were negligible. He stated that in his humble opinion, "Education is nothing less than the gradual unfolding of the faculties and powers which Providence chose to bestow on man." After founding several less-than-successful schools in the East, Neef moved to Louisville, Kentucky, in 1815. In Louisville, the last two of the Neef children were born. Neef had brought Josiah Warren with him as an assistant, but their Louisville school was not a success. Neef decided to give up teaching and moved his family to a farm in Shelby County, Kentucky.

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Again, at the urging of Maclure, Neef left his farm and came to New Harmony, Indiana, in March of 1826. In New Harmony, Neef was put in charge of the boarding school in Community House No. 2. Mrs. Neef taught in this school as did most of the scientists, including Gerard Troost, Thomas Say, Charles Alexandre Lesueur, and the three oldest Neef children. 

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Neef was a simple, straightforward, cordial man, who had a roughness about him. He was a good musician with a wonderful bass voice so strong it was said he could give commands to 10,000 troops. It was this voice, his fierce language, and his dreadful military profanity that frightened the children and probably kept them in line. Years later elderly adults well remembered the profound effect the boarding school had had on them. A simple man, Neef usually wore linen shirts with trousers and often went barefooted and bareheaded.

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When the Duke of Saxe-Weimer, also a native of Alsace, visited New Harmony, it was specifically to see Neef, of whom he had heard. After meeting Neef he wrote that he appeared aged (actually he was 58) and that he was still "full of the maxims of the French revolution. Neef talked of the emancipation of slaves, was captivated by the system of equality, and openly proclaimed himself an atheist."