Samuel Thomson (9 February 1769 – 5 October 1843) was a self-taught American herbalist and botanist, best known as the founder of the alternative system of medicine known as "Thomsonian Medicine", which enjoyed wide popularity in the United States during the 19th century.

From a young age he became curious about the various plants which he saw growing in the countryside and their medicinal uses. Much of his early knowledge was acquired from a local widow woman, who had acquired a reputation as a healer because of her skill with herbal remedies. Thomson also used to sample the plants he found growing in the wild—in this way he discovered Lobelia, which became an important remedy in the system of medicine he later founded. Unaware of the medicinal properties of the plant, Thomson used to trick other boys into eating it, which caused them to vomit because of its emetic nature.

At the age of sixteen he had hoped to study with a local "root" doctor (at that time there was no official licensing of the medical profession) but his parents did not think he had the education and could not spare him from his work. Thus, he became resigned to his life as a farm laborer. At the age of nineteen, while he was chopping wood, his ankle sustained a severe injury which, despite the ministration of a local doctor, refused to heal. His condition worsened and the family feared for his life. He decided to treat the wound himself with a comfrey root and turpentine plaster—after some weeks he was able to make a recovery.

At the age of 21, Samuel's father left for Vermont, placing Samuel in charge of the farm and leaving his mother and sister in his care. Soon after, his mother became ill with measles, and in spite of the efforts of several doctors, Samuel's mother died when the measles turned into "galloping consumption". When Samuel also became ill with measles, he cured himself using herbal remedies. One year later, Thomson married Susanna Allen on July 7, 1790 in Keene, New Hampshire. After the birth of their first child, Susanna became very ill, and a parade of seven conventional doctors were unable to cure her. Samuel arranged for two "root doctors" to treat his wife, who returned to health the next day. Thomson and Susanna went on to have eight children.

When his wife nearly died after being treated via conventional medicine, Thomson consulted two herbalists, who treated his wife and taught Thomson some of their methods. Subsequently, Thomson used steambaths and herbs to cure one of his daughters and a son, and a few of his neighbors. In this way, Thomson developed his own method, the Thomsonian System, and practiced in Surry, New Hampshire and the adjoining towns. During the first half of the 19th century his system had numerous followers, including some of his sons. It was based upon opening the paths of elimination so that toxins could be removed via physiological processes. This was not unique to Thomson: so-called "regular physicians" used calomel, a toxic mercury-based compound, to induce vomiting and purgation. Thomson's more moderate and less toxic means attracted large numbers of followers.

Eventually, Thomson came to believe that the exposure to cold temperatures was an important cause of illness and that disease should be treated by restoring the body's natural heat. Thomson's methods for doing this included steam baths, the use of cayenne pepper, laxatives, and administration of the emetic Lobelia inflata (also known as "Indian tobacco" or "puke weed").

Moreover, his system of medicine appealed to the egalitarian anti-elitist sentiments of Jacksonian America in the 1830s, and families far from established towns came to rely on it. At that time, licensed doctors and many of their methods such as bloodletting came under intense scrutiny, so Thomson's innovative system was presented as an appealing alternative that allowed each individual (working classes included) to administer his or her own treatment using natural products. A favorable opinion of his system was given by the contemporary physician Daniel Drake, who perceived him as an American medical reformist

Despite Thomson's popularity, some licensed doctors came to resent his work, and he was criticized for his techniques. On the one hand, some people who received his training broke with him and went on to pursue advanced medical education, founding Physio-Medicalism, while on the other hand, some of his former apprentices like Miler Comings, acknowledged him as an early great mentor. On the other hand, detractors like John Brown accused him of lack of anatomical and physiological knowledge, and they attributed Thomson's downfall to a relunctancy to interact more with doctors.