In 1836 when Eddy was fifteen, the Bakers moved twenty miles to Sanbornton Bridge, New Hampshire, known after 1869 as Tilton.

She was received into the Congregational church in Tilton on 26 July 1838 when she was 17, according to church records published by McClure's in 1907. Eddy had written in her autobiography in 1891 that she was 12 when this happened, and that she had discussed the idea of predestination with the pastor during the examination for her membership; this may have been an attempt to reflect the story of a 12-year-old Jesus in the Temple. She wrote in response to the McClure's article that the date of her church membership may have been mistaken by her. Eddy objected so strongly to the idea of predestination and eternal damnation that it made her ill:

Eddy was badly affected by four deaths in the 1840s. She regarded her brother Albert as a Teacher and mentor, but he died in 1841. In 1844, her first husband George Washington Glover (a friend of her brother Samuel's) died after six months of marriage. They had married in December 1843 and set up home in Charleston, South Carolina, where Glover had Business, but he died of yellow fever in June 1844 while living in Wilmington, North Carolina. Eddy was with him in Wilmington, six months pregnant. She had to make her way back to New Hampshire, 1,400 miles by train and steamboat, where her only child George Washington II was born on 12 September in her father's home.

Bates and Dittemore write that Eddy was not able to attend Sanbornton Academy when the family first moved there, but was required instead to start at the district school (in the same building) with the youngest girls. She withdrew after a month because of poor health, then received private tuition from the Reverend Enoch Corser. She entered Sanbornton Academy in 1842.

Her husband's death, the journey back, and the birth left her physically and mentally exhausted, and she ended up bedridden for months. She tried to earn a living by writing articles for the New Hampshire Patriot and various Odd Fellows and Masonic publications. She also worked as a substitute Teacher in the New Hampshire Conference Seminary, and ran her own kindergarten for a few months in 1846, apparently refusing to use corporal punishment.

Then her mother died in November 1849. Eddy wrote to one of her brothers: "What is left of earth to me!" Her mother's death was followed three weeks later by the death of her fiancé, Lawyer John Bartlett. In 1850, Eddy wrote, her son was sent away to be looked after by the family's nurse; he was four years old by then. Sources differ as to whether Eddy could have prevented this. It was difficult for a woman in her circumstances to earn money and, according to the legal doctrine of coverture, women in the United States during this period could not be their own children's guardians. When their husbands died, they were left in a legally vulnerable position.

George was sent to stay with various relatives, and Eddy decided to live with her sister Abigail. Abigail apparently also declined to take George, then six years old. Eddy married again in 1853. Her second husband, Daniel Patterson, was a dentist and apparently said that he would become George's legal guardian; but he appears not to have gone ahead with this, and Eddy lost contact with her son when the family that looked after him, the Cheneys, moved to Minnesota, and then her son several years later enlisted in the Union army during the Civil War. She did not see him again until he was in his thirties:

Phineas Quimby by 1859 had connected his healing practices with the Christ of the New Testament. He also called his method of healing the "science of health" and the "science of Christ," and had used the term "Christian Science" to describe his work. According to the Historian of science James C. Whorton, "In Quimby's mind, Christ and science were synonymous; his method of healing he thus called the Science of Christ and even, toward the close of his life, "Christian Science."

In October 1862, Eddy became a patient of Phineas Quimby, a magnetic healer from Maine. From 1862 to 1865, Quimby and Eddy engaged in lengthy discussions about healing methods practiced by Quimby and others. The extent to which he influenced her is much debated. Originally, Eddy gave Quimby much credit for his hypnotic treatments of her nervous and physical conditions and initially thought his brand of mesmerism entirely benign.

According to Gill, Eddy knew Spiritualists and took part in some of their activities, but was never a convinced believer. For Example, she visited her friend Sarah Crosby in 1864, who believed in Spiritualism. Eddy attempted to show Crosby the folly of it by pretending to channel Eddy's brother Albert and writing letters which she attributed to him.

Eddy was born Mary Morse Baker in a farmhouse in Bow, New Hampshire to farmer Mark Baker (d. 1865) and his wife Abigail Barnard Baker, née Ambrose (d. 1849). Eddy was the youngest of the Bakers' six children: boys Samuel Dow (1808), Albert (1810), and George Sullivan (1812), followed by girls Abigail Barnard (1816), Martha Smith (1819), and Mary Morse (1821).

Between 1866 and 1870, Eddy boarded at the home of Brene Paine Clark who was interested in Spiritualism. Seances were often conducted there, but Eddy and Clark engaged in vigorous, good-natured arguments about them. Eddy's arguments against Spiritualism convinced at least one other who was there at the time—Hiram Crafts—that "her science was far superior to spirit teachings." Clark's son George tried to convince Eddy to take up Spiritualism, but he said that she abhorred the idea. According to Cather and Milmine, Mrs. Richard Hazeltine attended seances at Clark's home, and she said that Eddy had acted as a trance medium, claiming to channel the spirits of the Apostles. Eddy was also known for channeling messages from the dead brother of her friend Sarah Crosby. According to Martin Gardner, Eddy's mediumship converted Crosby to Spiritualism.

Eddy devoted the rest of her life to the establishment of the church, writing its bylaws, The Manual of The Mother Church, and revising Science and Health. By the 1870s she was telling her students, "Some day I will have a church of my own." In 1879 she and her students established the Church of Christ, Scientist, "to commemorate the word and works of our Master [Jesus], which should reinstate primitive Christianity and its lost element of healing." In 1892 at Eddy's direction, the church reorganized as The First Church of Christ, Scientist, "designed to be built on the Rock, Christ...." In 1881, she founded the Massachusetts Metaphysical College, where she taught approximately 800 students between the years 1882 and 1889, when she closed it. Eddy charged her students $300 each for tuition. This was a large sum for the period and generated considerable controversy.

In 1872 Eddy had an argument with her student Richard Kennedy and he was expelled from Christian Science. Later she came to believe that he was using mental powers to destroy her so she ordered her students to "mobilize all their mental Energy to combat him". Eddy also ordered her students to stand outside her bedroom door to protect her from any mental attacks directed at her. In 1882 Eddy publicly claimed that her last husband, Asa Gilbert Eddy, had died of "mental assassination". Daniel Spofford was another Christian Scientist expelled by Eddy after she accused him of practicing malicious animal magnetism. According to Eugene V. Gallagher:

Eddy divorced Daniel Patterson for adultery in 1873. She published her work in 1875 in a book entitled Science and Health (years later retitled Science and Health with Key to the Scriptures) which she called the textbook of Christian Science, after several years of offering her healing method. The first publication run was 1,000 copies, which she self-published. During these years, she taught what she considered the science of "primitive Christianity" to at least 800 people. Many of her students became healers themselves. The last 100 pages of Science and Health (chapter entitled "Fruitage") contains testimonies of people who claimed to have been healed by reading her book. She made numerous revisions to her book from the time of its first publication until shortly before her death.

Mark Baker remarried in 1850; his second wife Elizabeth Patterson Duncan (d. 6 June 1875) had been widowed twice, and had some property and income from her second marriage. Baker apparently made clear to Eddy that her son would not be welcome in the new marital home. She wrote:

In 1877, she married Asa Gilbert Eddy; in 1882, they moved to Boston, and he died that year.

In 1888, a reading room selling Bibles, her writings and other publications opened in Boston. This model would soon be replicated, and branch churches worldwide maintain more than 1,200 Christian Science Reading Rooms today.

The belief in malicious animal magnetism "remains a part of the doctrine of Christian Science." In an article entitled "Malicious Animal Magnetism" published in the Christian Science Journal, February 1889, Eddy wrote that mental assassination was one of the greatest crimes and that anyone practicing it should be put to death by a human executioner. Several persons committed suicide because of the fear of malicious animal magnetism. Mary Tomlinson, a student of Mary Baker Eddy, committed suicide by throwing herself out of a window. Another Christian Scientist Marion Stephens committed suicide by gassing herself in a bathroom.

In the 24th edition of Science and Health, up to the 33rd edition, Eddy admitted the harmony between Vedanta philosophy and Christian Science. She also quoted certain passages from an English translation of the Bhagavad Gita, but they were later removed. According to Gill, in the 1891 revision Eddy removed from her book all the references to Eastern religions which her Editor, Reverend James Henry Wiggin, had introduced. On this issue Swami Abhedananda wrote:

In 1894 an edifice for The First Church of Christ, Scientist was completed in Boston (The Mother Church). In the early years Eddy served as pastor. In 1895 she ordained the Bible and Science and Health as the pastor.

Eddy founded The Christian Science Publishing Society in 1898, which became the publishing home for numerous publications launched by her and her followers. In 1908, at the age of 87, she founded The Christian Science Monitor, a daily newspaper. She also founded the Christian Science Journal in 1883, a monthly magazine aimed at the church's members and, in 1898, the Christian Science Sentinel, a weekly religious periodical written for a more general audience, and the Herald of Christian Science, a religious magazine with editions in many languages.

Eddy recommended to her son that, rather than go against the law of the state, he should have her grandchildren vaccinated. She also paid for a mastectomy for her sister-in-law. Eddy was quoted in the New York Herald on 1 May 1901: "Where vaccination is compulsory, let your children be vaccinated, and see that your mind is in such a state that by your prayers vaccination will do the children no harm. So long as Christian Scientists obey the laws, I do not suppose their mental reservations will be thought to matter much."

A diary kept by Calvin Frye, Eddy's personal secretary, suggested that Eddy had a lifelong dependence on morphine. Miranda Rice, a friend and close student of Eddy, told a newspaper in 1906: "I know that Mrs. Eddy was addicted to morphine in the seventies. She begged me to get some for her. She sent her husband Mr. Eddy for some, and when he failed to get it went herself and got it. She locked herself into her room and for two days excluded every one. She was a slave to morphine." Gillian Gill writes that the prescription of morphine was normal medical practice at the time.

A 1907 article in the Journal of the American Medical Association noted that Eddy exhibited hysterical and psychotic behaviour. Psychiatrist Karl Menninger in his book The Human Mind (1927) cited Eddy's paranoid delusions about malicious animal magnetism as an Example of a "schizoid personality".

Eddy died of pneumonia on the evening of December 3, 1910 at her home at 400 Beacon Street, in the Chestnut Hill section of Newton, Massachusetts. Her death was announced the next morning, when a city medical examiner was called in. She was buried on December 8, 1910 at Mount Auburn Cemetery in Cambridge, Massachusetts. Her memorial was designed by New York Architect Egerton Swartwout (1870-1943). Hundreds of tributes appeared in newspapers around the world, including The Boston Globe, which wrote, "She did a wonderful—an extraordinary work in the world and there is no doubt that she was a powerful influence for good."

In 1921, on the 100th anniversary of Eddy's birth, a 100-ton (in rough) and 60–70 tons (hewn), pyramid with a 121 square foot footprint was dedicated on the site of her birthplace in Bow, New Hampshire. A gift from James F. Lord, it was dynamited in 1962 by order of the church's board of Directors. Also demolished was Eddy's former home in Pleasant View, as the board feared that it was becoming a place of pilgrimage.

Wendell Thomas in Hinduism Invades America (1930) suggested that Eddy may have discovered Hinduism through the teachings of the New England Transcendentalists such as Bronson Alcott. Stephen Gottschalk, in his The Emergence of Christian Science in American Religious Life (1973), wrote:

Eddy and her father reportedly had a volatile relationship. Ernest Sutherland Bates and John V. Dittemore wrote in 1932 that Baker sought to break Eddy's will with harsh punishment, although her mother often intervened; in contrast to Mark Baker, Eddy's mother was described as devout, quiet, light-hearted, and kind. Eddy experienced periods of sudden illness, perhaps in an effort to control her father's attitude toward her. Those who knew the family described her as suddenly falling to the floor, writhing and screaming, or silent and apparently unconscious, sometimes for hours. Robert Peel, one of Eddy's biographers, worked for the Christian Science church and wrote in 1966:

Psychologists Leon Joseph Saul and Silas L. Warner, in their book The Psychotic Personality (1982), came to the conclusion that Eddy had diagnostic characteristics of Psychotic Personality Disorder (PPD). In 1983, Psychologists Theodore Barber and Sheryl C. Wilson suggested that Eddy displayed traits of a fantasy prone personality.

Gillian Gill wrote in 1998 that Eddy was often sick as a child and appears to have suffered from an eating disorder, but reports may have been exaggerated concerning hysterical fits. Eddy described her problems with food in the first edition of Science and Health (1875). She wrote that she had suffered from chronic indigestion as a child and, hoping to cure it, had embarked on a diet of nothing but water, bread, and vegetables, at one point consumed just once a day: "Thus we passed most of our early years, as many can attest, in hunger, pain, weakness, and starvation."

The converse of mental healing was the use of mental powers to destroy people's health – what Eddy termed "malicious animal magnetism." She was concerned that a new practitioner could inadvertently harm a patient through unenlightened use of their mental powers, and that less scrupulous individuals could use such powers as a weapon.

Eddy wrote that her father had been a justice of the peace at one point and a chaplain of the New Hampshire State Militia. He developed a reputation locally for being disputatious; one neighbor described him as "[a] tiger for a temper and always in a row." McClure's reported several similar stories from neighbors, including that he once killed a crow with his walking stick for violating the Sabbath. The magazine described him as a supporter of slavery and alleged that he had been pleased to hear about Abraham Lincoln's death. Eddy responded that Baker had been a "strong believer in States’ rights, but slavery he regarded as a great sin."