He was born in 1736 at an estate known as Chestnut Hill on the banks of the James River in Virginia, a place at which his elder brother would later establish the town of Lynchburg.
Lynch's father left his native Ireland and emigrated to the English Colony of Virginia in about 1725 as an indentured servant, called a "redemptioner" in the nomenclature of the day. Upon arrival to the New World, Lynch's contract of indenture was sold to a wealthy planter living in Caroline County. Lynch remained with the planter for his fixed term of servitude, winning in the process not only his freedom but also the hand of his daughter, Sarah Clark, in marriage.
With the financial assistance of the elder Clark, the Lynches themselves became planters of tobacco on a large scale, farming well over 7,000 acres of Virginia land. Sometime between Charles' birth in 1736 and the middle of the decade, Charles' father died, leaving behind his Chestnut Hill estate to his eldest son, John. His mother joined the Quaker religious sect in 1750, bringing her sons with her into that religion.
Lynch married a fellow Quaker, the former Anne Terrell, on January 12, 1755. With Chestnut Hill occupied by his brother, the young couple set out to establish their new home on Virginia's western frontier on a more distant parcel of land granted to his father by King George II, in the newly established Bedford County. Green Level, the Lynch estate where the couple would ultimately raise five children, was located at a place now marked by the town of Altavista.
Lynch was instrumental in organizing a Quaker meeting in Bedford County and raising funds for a building to house it, the first public house of worship in the area. Lynch served for several years as the clerk of the meeting and as trustee of the group's meeting house. He was also a delegate to the Quaker Assembly in Virginia.
Following the end of the French and Indian War in 1763, the danger associated with life at the frontier greatly lessened, and a flood of newcomers began to appear in Bedford County. His position as a landowner and leading citizen was now well-established. His farming of tobacco and raising of cattle had made him a wealthy man, the possessor of property and African slaves. Beginning in 1764 other citizens began to approach Lynch to ask him to become a candidate for the Virginia Assembly. Lynch initially refused the entreaties on the grounds that swearing the necessary oath of office was prohibited behavior for an adherent of the Quaker religion.