Thacher was born in Ballston, New York, graduated from Williams College in 1869 and settled in Albany, New York. He became an active scholar in writing after college and also became active in his father's business, the Thacher Car Wheel Works, which was one of the leading industries in Albany. When his father died in 1887, John and his brother George became proprietors of the business. Thacher was the father of Ebby Thacher, who was regarded as the man who brought Bill Wilson, founder of Alcoholics Anonymous, into the Oxford Group, which was the model for the later fellowship for alcoholics.