John White Webster was born on May 20, 1793, in Boston, Massachusetts. He came from a well-connected family. His grandfather was a successful merchant. His mother, Hannah White Webster, was part of a notable Harvard dynasty and was a descendant of John Leverett, an early governor of the Massachusetts Bay Colony. Webster's wife, Harriet Fredrica Hickling, came from a wealthy family as well. Her sister married into the Prescott family, which included descendants of William Prescott, a leader during the American Revolution. Webster was friends with prominent figures, including Robert Gould Shaw, and was associated with influential people in his community.

Webster graduated from Harvard College in 1811. In 1814, he became one of the founders of the Linnaean Society of New England. He also took on the role of cabinet-keeper for the society's growing collection of specimens in Boston. Around 1815, he moved to London for further studies. There, he worked at Guy's Hospital as a surgeon's pupil and in various medical roles. He later moved to São Miguel Island in the Azores from 1817 to 1818. On the island, he practiced medicine, published his first book, and married Harriet Hickling on May 16, 1818. Together, they had four daughters.

After returning to Boston, Webster tried to build a private medical practice but struggled to find success, leading him to change careers. In 1823, he was elected a Fellow of the American Academy of Arts and Sciences. The following year, he was appointed as a lecturer of chemistry, mineralogy, and geology at Harvard Medical College. In 1827, he became the Erving professor. He lived on Common Street in Boston.

At Harvard, Webster was known as an engaging lecturer, described as "pleasant" yet "nervous and excitable." His teaching included many demonstrations of new chemical discoveries. He was noted for interesting classroom experiments, including making solid carbon dioxide. Webster was also remembered for creating a lively atmosphere in the classroom with fireworks and demonstrations, although some were viewed as dangerous. He wrote several academic texts, including "A Description of the Island of St. Michael" and a manual on chemistry, which received positive reviews from noted scientists of the time.

On November 23, 1849, Dr. George Parkman was murdered. John White Webster was accused of this murder on January 26, 1850. The case went to trial and was considered a major event in the legal community at that time. It marked one of the first uses of forensic evidence in America, as the remains of Dr. Parkman were partially cremated. Investigators used dental records and bone fragments to identify the remains as belonging to Dr. Parkman.

The trial gained a lot of media attention, especially because Webster worked as a professor at Harvard University. Evidence suggested that Webster was in debt to Parkman and that they had disagreements over money. During the trial, Webster was not allowed to testify in his own defense, a rule under the law in Massachusetts at that time. The judge, who was a relative of Parkman, instructed the jury they "must" return a guilty verdict. Despite the judge’s reminders about reasonable doubt, much of the evidence that could have helped Webster was either not presented or was rejected.

After the trial, Webster was found guilty. He was sentenced to death and taken to Leverett Street Jail in Boston. On August 30, 1850, he was publicly hanged. This case remained significant and has been discussed in various media, emphasizing its historical importance.