Stephens was born in Shrewsbury, New Jersey. He studied at Columbia University where he obtained a law degree. In 1834, he traveled to the Near East and later wrote a book describing his travels.
Stephens wrote several popular books about his travels and explorations:
In 1839, President Martin Van Buren commissioned Stephens as Special Ambassador to Central America. While there, the government of the United States of Central America fell apart in civil war. "Incidents of Travel in Central America, Chiapas and Yucatan" gives a vivid description of some of those events which Stephens witnessed. Of even greater importance, it provided descriptions of several ancient Maya sites, along with illustrations by Stephen's traveling companion, architect and draftsman Frederick Catherwood. These were greatly superior in both amount and accuracy of depection to the small amount of information on ancient Mesoamerica previously published. Stephens continued his investigations of Maya ruins with a return trip to Yucatan which produced a further book.
In 1850 he traveled to Panama to work on the project to construct a trans-isthmus railroad, where he died of malaria in 1852 before the Panama Railway's completion.
Stephens is the subject of a biography Maya Explorer by Victor Wolfgang Von Hagan, first published in 1947.