Born in Haverhill, Massachusetts, Greene was the son of the Democratic journalist and Boston postmaster Nathaniel Greene. He was appointed to the United States Military Academy from Massachusetts in 1835, but he left before graduation. He was made 2nd lieutenant in the 7th infantry in July 1839 and after serving in the second Seminole War resigned in November 1841. Subsequently, he was connected with George Ripley's utopian movement at Brook Farm, after which he met several transcendentalists including Orestes Brownson, Elizabeth Peabody and Ralph Waldo Emerson. He studied theology at Harvard Divinity School, graduating in 1845. He was a pastor at a Unitarian church in Brookfield, Massachusetts before leaving to Europe.