Lindley was sent to an academy in Canonsburg, Pennsylvania at the age of eighteen, which subsequently became Jefferson College. A few years later he entered the College of New Jersey, having traveled the entire distance from the Monongahela River by the "ride and tie" method in company with James Carnahan, destined to become the ninth president of that institution. He graduated in 1800.
Lindley was licensed to preach by the Washington County Presbytery in 1800. In 1803 he settled as pastor of the church at Waterford, Ohio. Two years later he was appointed trustee of the, as yet, non-existent Ohio University. Unlike some of his fellow appointees he took from the first an active interest in the affairs of the prospective institution. On April 2, 1806, he was made member of a committee "to contract with some person or persons for building a house in the town of Athens for the purpose of an academy on the credit of rents that will hereafter become due" (from the two townships of land granted to the University). On the completion of this building Lindley was appointed to a committee "to report a plan for opening and conducting an academy and providing a preceptor. " A few days later he was himself elected preceptor and entered upon his duties in the spring of the same year, 1808.
For the first four years he was the sole instructor in the only department of the University then existing, the preparatory department. By 1822 the institution was in a position financially to make possible the provision for instruction of college grade. A college faculty was organized in which Lindley was assigned to the chair of mental and moral philosophy and belles-lettres. Two years later, in 1823, he was transferred to the chair of mathematics, which position he held until 1826. With his scholastic duties he apparently combined those of pastor of a Presbyterian church established there in 1809 largely through his influence. Although there is no evidence that he possessed unusual talent as teacher, administrator, or scholar, he seems nevertheless to have been the moving spirit in inaugurating the activities of the first university to be founded on a grant made by the federal government.
In 1828 he took charge of a church at Walnut Hills, near Cincinnati, but in 1829 he removed to Grave Creek in Virginia and shortly afterward to Pennsylvania. After he had left the state, the legislature appointed Thomas Bryce to his seat on the board of trustees of the university. Lindley contested the action (1836) and won his suit, but he resigned from the board two years later upon removing to the South. Finally he returned to Connellsville, Pennsylvania, where he died at the residence of his son, Dr. Lutellus Lindley, in 1857. At the solicitation of his daughters and some other young mothers Lindley published at Uniontown, Pennsylvania, in 1846, a little treatise on the training of children entitled Infant Philosophy. The work is characterized chiefly by the importance it attaches to the education of children while still very young, below three years of age, and by its vigorous attack on Locke's "tabula rasa" theory.
In 1800 Lindley married Hannah Dickey. They had nine children.