Benjamin Banneker was born on November 9, 1731, in Baltimore County, Maryland to Mary Banneky, a free black, and Robert, a freed slave from Guinea.

In 1737, Banneker was named at the age of 6 on the deed of his family's 100-acre (0.40 km2) farm in the Patapsco Valley in rural Baltimore County.

Around 1753 at about the age of 21, Banneker reportedly completed a wooden clock that struck on the hour. He appears to have modeled his clock from a borrowed pocket watch by carving each piece to scale. The clock purportedly continued to work until his death.

After his father died in 1759, Banneker lived with his mother and sisters.

In 1768, he signed a Baltimore County petition to move the county seat from Joppa to Baltimore. An entry for his property in a 1773 Baltimore County tax list identified Banneker as the only adult member of his household.

In 1772, brothers Andrew Ellicott, John Ellicott and Joseph Ellicott moved from Bucks County, Pennsylvania, and bought land along the Patapsco Falls near Banneker's farm on which to construct gristmills, around which the village of Ellicott's Mills (now Ellicott City) subsequently developed. The Ellicotts were Quakers and shared the same views on racial equality as did many of their faith. Banneker studied the mills and became acquainted with their proprietors.

In 1788, George Ellicott, the son of Andrew Ellicott, loaned Banneker books and equipment to begin a more formal study of astronomy. During the following year, Banneker sent George his work calculating a solar eclipse.

In 1790, Banneker prepared an ephemeris for 1791, which he hoped would be placed within a published almanac. However, he was unable to find a printer that was willing to publish and distribute the work.

In February 1791, surveyor Major Andrew Ellicott (the son of Joseph Ellicott and cousin of George Ellicott), having left at the request of U.S. Secretary of State Thomas Jefferson a surveying team in western New York that he had been leading, hired Banneker as a replacement to assist in the initial survey of the boundaries of a new federal district. Formed from land along the Potomac River that the states of Maryland and Virginia ceded to the federal government of the United States in accordance with the 1790 federal Residence Act and later legislation, the territory that became the original District of Columbia was a square measuring 10 miles (16 km) on each side, totaling 100 square miles (260 km2). Ellicott's team placed boundary marker stones at or near every mile point along the borders of the new capital territory.

Banneker left the boundary survey in April 1791 within three months of its initiation because of concerns about his health and the difficulties in completing the survey at age 59. In addition, Andrew Ellicott's younger brothers, Benjamin and Joseph Ellicott, who usually assisted Andrew, were able to join the survey at that time. Banneker therefore returned to his home near Ellicott's Mills. The Ellicotts and other members of the surveying team then laid the remaining Virginia marker stones later in 1791. The team laid the Maryland stones and completed the boundary survey in 1792.

An April 21, 1791, news report of the April 15 dedication ceremony for the first boundary stone (the south cornerstone) stated that it was Andrew Ellicott who "ascertained the precise point from which the first line of the district was to proceed". The news report did not mention Banneker's name.

On August 19, 1791, after departing the federal capital area, Banneker wrote a letter to Thomas Jefferson, who in 1776 had drafted the United States Declaration of Independence and in 1791 was serving as the United States Secretary of State.

Banneker's 1792 almanac contained an extract from an anonymous essay entitled "On Negro Slavery, and the Slave Trade" that the Columbian Magazine had published in 1790.

Banneker kept a series of journals that contained his notebooks for astronomical observations, his diary and accounts of his dreams. The journals, only one of which escaped a fire on the day of his funeral, additionally contained a number of mathematical calculations and puzzles. The surviving journal described in April 1800 Banneker's recollections of the 1749, 1766 and 1783 emergencies of Brood X of the seventeen-year periodical cicada, Magicicada septendecim, and stated, "... they may be expected again in they year 1800 which is Seventeen Since their third appearance to me." The journal also recorded Banneker's observations on the hives and behavior of honey bees.

Banneker never married. Because of declining sales, his 1797 almanacs were the last that printers published. After selling much of his homesite to the Ellicotts and others, he probably died in his log cabin nine years later on October 19, 1806, aged 74.