Like other parts of Lincoln’s personal life, the answer is ambiguous. Theists and non-theists can claim him at different times in his life, though neither side will be entirely satisfied.
Gerald Prokopowicz, author of Did Lincoln Own Slaves?: And Other Frequently Asked Questions About Abraham Lincoln, answers the question:
Lincoln didn’t leave many clues about his views on Sabbatarianism, or on religion in general. His father had been a member of the Little Pigeon Creek Baptist church, and Lincoln must have been exposed to doctrines like predestination at an early age, but he never joined the Baptist church… We know that it was at this time in his life that Lincoln read Thomas Paine’s Age of Reason, and probably the works of Voltaire and other Enlightenment skeptics. By the time he moved to Springfield in 1837, he had begun to develop his unique world view, a mixture of skepticism and providential fatalism that would continue to mature and evolve throughout his life.
Wasn’t he secretly baptized when he was older?
No, nor was he planning to convert to (fill in the church of your choice) on Easter Sunday, 1865, only to be tragically murdered on the preceding Good Friday.
The answers to questions about Lincoln’s church membership are not the ones that most people are hoping to hear. He was never a member of the church you attend, or any church. His religious beliefs were dynamic, complex, and powerful, but not conventional. He wasn’t a Baptist, despite being raised in a Baptist tradition. He wasn’t a Presbyterian, although he attended Presbyterian services much of his adult life. He was not a Catholic… According to Mrs. Lincoln, who ought to have known, he was not even a Christian…If Lincoln wasn’t a Christian, why are his speeches full of talk about God?
Because he believed in God, or Providence, or some kind of supernatural power beyond this earth that controlled the fates of people and nations…
Lincoln’s ideas, whatever they were, were not easy to grasp. While he accepted the notion of providence, and referred to it often, he rarely spoke publicly of Jesus Christ. In New Salem Lincoln associated with freethinkers who doubted the divinity of Jesus, and he wrote an essay mocking the idea that Jesus was the son of God. Lincoln’s friends, anxious to protect his budding political career, threw the manuscript into the fire…
Lincoln became more religious later in his life, but no evidence points to any conversion process.
A couple anecdotes “reveal Lincoln’s greater willingness to accept some of the ideas and sources of traditional Christianity, but they fall far short of implying any kind of conversion experience.”
(via Change of Subject)
(Thanks to Laramie for the link!)