Jack's application to Choate was filled out by his mother in May of 1929. After taking the entrance examinations, Kenned was accepted. Then, his mother, changed her mind and decided instead to send Jack to a Catholic boarding school, called Canterbury. The Canterbury School was small, with fewer than 100 students. In an early letter, Jack wrote, " It's a pretty good place, but I was pretty homesick the first night. " 1 Jack continued to be homesick. His father wanted to transfer him to Choate, but his mother continued to oppose the idea. Jack worked hard at school, earning grades of 95 in English; 93 in Math; 80 in History; 78 in Science; and a 68 in Latin. It was not long, however, until he became sick.

One day, he collapsed in church. Jack began to lose weight, along with his ability to concentrate. He went to Palm Beach for Easter vacation to recuperate, but on his return to school he collapsed once again. Jack was diagnosed with appendicitis. An operation was performed, but Jack's recovery was long and difficult. He did not complete the year. Instead Jack took his exams at home.

In the following year of 1931, Jack finally went to Choate. His brother, Joe, was already a junior there. Jack had a difficult time adjusting to Choate. Following rules was not his strong point. In addition, Choate required as two of his core subjects that first term, Latin and French, with which he had had the greatest difficulty in the past.  Jack fell sick once again at Choate and spent a great deal of time in the infirmary. He did not do well academically during his first year. He failed the end of the year exams in French and Latin. Jack spent the following months in summer school at Choate.

During the next academic year, Jack continued at Choate. He continued to be sick, with strange flu-like symptoms, as well as other health problems. He worked hard at his studies and did well, but was eclipsed by his brother's stellar performance. Joe Jr. won the Harvard award, given for the best combination of scholarship and sportsmanship.

In his third year, Jack had a new house master; J. J. Maher. Maher was considered a strong disciplinarian. Jack and Maher did not get along and were constantly at odds with one another. His fights with Maher came to an end, when he was confined to the school infirmary once again. This time, however, his illness was more serious. He was sent to a New Haven hospital, where his condition continued to deteriorate. Jack spent more than a month in the hospital. His illness was never definitively diagnosed. Jack spent the rest of the semester recuperating in Palm Beach. He returned to school after Easter, but continued to be a serious thorn in the side of the house master. One of his friends Lem Billings, recalled of Jack: " I"ve never known anyone in my life with such wonderful humor, the ability to make one laugh and have a good time. Boys who are as full of fun and ˜joie de vivre" as he was, can€™t help but irritate teachers. He was not very popular with the faculty. He did strive to succeed, always both competing with his brother on one hand, and with his father's expectations that "second best" was never best enough for a Kennedy boy. "  

Jack had planned to spend the summer of 1934 sailing at Cape Cod with his friend Lem Billings. Once again, however, he became sick. This time, his father decided to send him to the famed Mayo Clinic in Rochester Minnesota to find out what was wrong. After an extensive stay, they were no more able than anyone else, to discover what ailed him.  

In his senior year at Choate, Jack became more of a prankster. He organized a group of twelve fellow students, which called itself the " Muckers" . They carried out a series of practical jokes. Finally, the headmaster, George St. John decided that enough was enough. The decision was made to expel the whole group. However, after announcing their expulsion, he relented. He did, however, call in Jack's father for a conference.

Jack completed the year, and, in what was to be his first political campaign, was elected by his classmates as the " most likely to succeed" . That confidence was shared by the Headmaster who wrote to his father: " I never saw a boy with as many fine qualities as Jack has, [who] didn't come out right in the end. " Jack graduated number 65 in a class of 110, but given that his father and grandfather were Harvard graduates, and that his brother was already at Harvard, his entry into Harvard was virtually guaranteed.