Refusing to follow his uncle's wishes to become a clergyman, Pemberton pursued a teaching career that would become his life's work.

Consequently, due to his uncle's connections with the school, Pemberton attended Princeton University, then called the College of New Jersey, and graduated in 1765, valedictorian of his class.

"[12] Pemberton also supposedly tried his hand at law, admitted to the Bar of Rhode Island in 1777, but equally disliked the practice as he did the clergy.

Once he was allowed the option to resign, he accepted, receiving a salary of £140, succeeding Eliphalet Pearson as the second Principal in 1786.

He "maintained strict discipline" and ran the day's schedule "with perfect smoothness" while only using force as a last resort.

"[17] Caleb Strong, then Governor of Massachusetts, reported back to Judge Phillips: "My son's manners are much improved.

"[16] Pemberton also improved the curriculum, introducing courses in geography, higher levels of math, and public speaking.

Students, as was regular at the time, often read passages from the Bible during class, engaged in related exercises Monday afternoons, and attended mass at the South Church down the street on Sundays.

[18] Judge Phillips was pleased with Pemberton's work, as he writes in a letter dated July 26, 1790, to John Phillips: "This Academy is in a more flourishing state than it has been for some time — its numbers before the vacation about 54 — twelve in the Sen'r class well fitted for college tho' but 7 have yet been offered for admission — the morals and deportment of the youths regular.

One of his gifts included a sum of more than $20,000 in October 1789 in order to increase access of the school to students of poor families.

In John Phillips' words, "for and in consideration of further promoting the virtuous and pious education of youth (poor children of genius, and of serious disposition especially)"[20] One of the most notable moments of Pemberton's administration was President George Washington's visit to Phillips Academy on November 5, 1789, during his tour of the Eastern States.

[21] That afternoon the President held an informal reception on what was then the training field, now the site of the Memorial Bell Tower.

He wrote a letter of resignation on October 9, 1793 which was delayed by the Trustees to December 24 with the hope his health might improve.

They were reluctant to let go of Pemberton too soon, as he had only been principal for seven years and had been praised for his "ability, attention, and fidelity" as quoted from the Trustees themselves.

[23] Claude Fuess, 10th Headmaster of Phillips Academy, describes Pemberton in his history of the school in 1917 with the following lines from William Wordsworth's The Excursion: "They, who were about him, did not fail In reverence, or in courtesy; they prized His gentle manners: and his peaceful smiles, The gleams of his slow-varying countenance, Were met with answering sympathy and love.

They were surprised that, despite claiming poor health as the reason for resigning from Phillips Academy, he would become principal of a school in Billerica, Massachusetts the next year.

When a group of Boston men pledged their support, he opened a small school in that city at 338 Washington Street for young children.

One of his former students, General Henry K. Oliver, writes:[26] "A man he was of the most refined and graceful manners; dignified, yet courteous in demeanor, pleasant of speech, accurate in language, pure in thought and life, conscientious in all he said and did, presenting himself to my memory as a living model of a Christian gentleman and godly man."

One of their students, writer Ednah Dow Littlehale Cheney, recalls Pemberton teaching her how to read in 1830.

Fuess concludes in his biography of Pemberton, "As Principal...he performed valuable service, but he was never fully praised during his period of labor, and his last days were a pathetic end for a life of sacrifice.