Benjamin Lincoln was born on January 24, 1733, in Hingham, Province of Massachusetts Bay the sixth child and first son of Colonel Benjamin Lincoln and his second wife Elizabeth Thaxter Lincoln. Lincoln's ancestors were among those who first settled in Hingham, beginning with Thomas Lincoln 'the cooper,' who was among several Lincolns who settled in Hingham when it was part of the Massachusetts Bay Colony. Lincoln's father, one of the wealthiest men in Suffolk County, served as a member of the governor's council from 1753 until 1770, and occupied many other civic posts before his death in 1771. Lincoln's maternal grandfather, Col. Samuel Thaxter, one of the most prominent and influential citizens in Hingham, became Colonel in a regiment and one of those commissioned to settle the boundary between Massachusetts and Rhode Island in 1719.

In his early life, Lincoln worked on the family farm, and attended the local school. He followed his father into public life, becoming town constable at 21, and in 1755 he joined the 3rd Regiment of the Suffolk County militia (where his father was colonel) as an adjutant. In 1756, at the age of 23, Lincoln married Mary Cushing, daughter of Elijah Cushing of Pembroke, Massachusetts, whose ancestors were also among the founders of Hingham. They had eleven children, seven of which survived to adulthood. In 1757, he was elected the town clerk of Hingham, a post he held for twenty years. He continued to be active in the militia during the French and Indian War, but saw no action, and was promoted to major by the end of the conflict in 1763.

Lincoln was elected a Hingham town selectman in 1765, a post to which he held for six years. During this tenure political opposition rose in the province to Parliamentary tax measures, polarizing the political landscape of the colony. Lincoln sided with the opposition, eventually becoming a leading force among Hingham's Patriots. In 1770, in a list of resolutions passed by the inhabitants of Hingham, Lincoln outlined the measures urged by residents towards the non-importation of British goods, and he condemned the Boston massacre. In 1772, Lincoln was promoted to lieutenant colonel of the 3rd Regiment of the Suffolk militia. That same year he won election as a representative of the town to the provincial assembly.

With the arrival of General Thomas Gage as governor of the colony in 1774, the provincial assembly was dissolved, but reformed itself into the Massachusetts Provincial Congress. Lincoln continued to win election to this body, and was placed on committees overseeing militia organization and supply, a position that came to be of utmost importance when the American Revolutionary War broke out with the Battles of Lexington and Concord in April 1775. He was then appointed to the congress' committee of safety, and also was elected to its executive council, which exercised executive authority over the province outside besieged Boston. He was deeply involved in ensuring that supplies of all sorts reached the nascent Continental Army outside Boston, procuring supplies from blankets to gunpowder.

Despite his lack of combat experience, Lincoln began lobbying state representatives to the Continental Congress for a Continental Army officers commission, anticipating that the aging and ill General Ward might soon step down. The idea was generally well received, with one representative writing that Lincoln was "a good man for a Brigadier General" and "a man of abilities", even though he had not "had much experience". While a Continental commission was not immediately forthcoming, Lincoln was placed in command of a brigade of militia the state sent to join General George Washington at New York Town in September 1776.

Lincoln's first command was that of a forward outpost at Bound Brook, New Jersey, only 3 miles (4.8 km) from British sentries outside New Brunswick. He established his headquarters at the nearby Van Horne House. After months of skirmishing, his post was the target of a surprise attack on April 13, 1777. In the Battle of Bound Brook he was defeated by a much larger force under the command of Lord Cornwallis, barely escaping capture.

Lincoln was transported to Albany, where he was treated, and where he learned of Burgoyne's October 17 surrender. His son helped him return him to Hingham in February 1778, where he convalesced for several months. The injury left his right leg two inches shorter than the left, and for many years the ankle wound was prone to reopening and the danger of infection. During his recovery Lincoln learned that General Arnold's seniority had been restored, reducing Lincoln to the lowest-ranked major general. Although he considered resignation over the slight, Washington and supporters in the Continental Congress assured him of his value to the army.

Lincoln rejoined Washington outside New York in August 1778, and was appointed commander of the Southern department in September. Washington sent Lincoln, Lafayette and Lee (Henry "Light Horse Harry") to the Southern Department to oppose the British army under Clinton and Cornwallis. Lincoln participated in the unsuccessful French-led siege of Savannah, Georgia in October 1779, after which he retreated to Charleston, South Carolina. He took command of the garrison of Charleston. In March 1780 the city was surrounded by a sizable British force dispatched from New York. After a relatively brief siege Lincoln was forced to surrender more than 5,000 men to Lieutenant General Sir Henry Clinton on May 12, 1780, but did so in a way that allowed the South Carolina militia to escape as well as some Continental forces, that annoyed the British toward Lincoln.

From 1781 to late 1783, Lincoln served as the first United States Secretary of War. He was appointed by the Confederation Congress under the Articles of Confederation and Perpetual Union, adopted 1781. He was succeeded in the post by Continental Army artillery chief, Gen. Henry Knox, (who later continued in the position under the new Federal Constitution of 1787, with first President George Washington, during his first term, 1789-1795). He was elected a Fellow of the American Academy of Arts and Sciences in 1781.

In 1787, Lincoln was a member of the Massachusetts state convention that ratified the United States Constitution. Earlier in 1787, Lincoln helped put an end to an uprising of farmers known as Shays' Rebellion. The uprising, one of whose consequences was increased calls for a stronger central U.S. government, ended when Lincoln's militia attacked the rebels and forced them to surrender in February.

He stayed active in public life in various capacities, including a term as Lieutenant Governor of Massachusetts and many years as the Collector of the Port of Boston. He retired from public life in 1809 and died in Hingham on May 9, 1810.

Lincoln's lifelong home still stands. It was declared a National Historic Landmark in 1972, and is listed on the National Register of Historic Places.

Places named "Lincoln" in the American South tend to be named after Benjamin Lincoln rather than Abraham Lincoln, the 16th President (the two were not related). Counties and/or towns in Alabama, Georgia, Kentucky, Missouri, North Carolina, and Tennessee are named in his honor, as are communities in North Carolina (Lincolnton), Vermont (Lincoln), and Maine (Lincolnville). Streets in Columbia, South Carolina and Savannah, Georgia bear his name, as does Lincoln Hall at the United States Coast Guard Training Center in Yorktown, Virginia.