Lynch received a good academic education at the Indigo Society School, Georgetown, then went to England where he completed his education at Eton and Cambridge and studied law at the Middle Temple from 1764 to 1772.
In 1772, Lynch went to South Carolina. Having acquired a distaste for the law, he persuaded his father to permit him to abandon that profession. This task was easier because his father had formed the design of introducing him to public life. To promote this object, he presented him with Peach Tree plantation in St. James Parish on the North Santee. Thomas Lynch settled down as a planter.
Being the only son of a wealthy and influential father, he was elected to many important civil offices. He was a member of the first and second provincial congresses (1774 - 1776), of the constitutional committee for South Carolina (1776), the first state General Assembly (1776), and the Second Continental Congress (1776 - 1777). On June 12, 1775, the provincial congress elected him one of the captains in the 1st South Carolina Regiment. He accepted the command, somewhat in opposition to the wishes of his father, who offered to use his influence to obtain him a military appointment of higher rank. In July he went into North Carolina to recruit his company. During this service he contracted bilious fever which made him a partial invalid for the remainder of his life. On March 23, 1776, the General Assembly of South Carolina, organized under the constitution which young Lynch had cooperated in drafting, elected him to the Continental Congress as a sixth delegate in order that he might care for his father, whose health had given way. His own health was too feeble to permit continued activity in public concerns, but he was present and voting when the Declaration of Independence was adopted and shortly afterward affixed his signature to that document. He did not remain long in Congress, for his health began to decline with alarming rapidity. The elder Lynch had experienced a temporary recovery and his physicians hoped he might live to reach Carolina.
Father and son began the journey homeward by easy stages, but the father died on the way. The younger Lynch reached his native state, but in a physical condition which did not promise a long continuance of his own life. After more than two years of illness, with the hope of possibly regaining health, he and his wife took passage for the West Indies toward the close of 1779, expecting to board a vessel there for the south of France. The ship on which they sailed was never heard of again and it is probable that all on board were lost.
Lynch married Elizabeth Shubrick on May 14, 1772.