Jenney was born in Fairhaven, Massachusetts on September 25, 1832, son of William Proctor Jenney and Eliza LeBaron Gibbs. Jenney first began his formal education at Phillips Academy, Andover, in 1846, and at the Lawrence Scientific school at Harvard in 1853, but transferred to l'École Centrale des Arts et Manufactures in Paris to get an education in engineering and architecture. He graduated in 1856, one year after his classmate, Gustave Eiffel, the designer of the Eiffel Tower. In 1861, he returned to the US to join the Union Army as an engineer in the Civil War, designing fortifications for Generals Sherman and Grant. By the end of the war, he had become a major, and was Engineer-in-Charge at Nashville's Union headquarters. After the war, in 1867, Jenney moved to Chicago, Illinois and began his own architectural office, which specialized in commercial buildings and urban planning.
During the late 1870s, he commuted weekly to Ann Arbor, Michigan to start and teach in the architecture program at the University of Michigan. In later years future leaders of the Chicago School like Louis Sullivan, Daniel Burnham, William Holabird, and Martin Roche, performed their architectural apprenticeships on Jenney's staff. On May 8, 1867, Jenney and Elizabeth "Lizzie" Hannah Cobb, from Cleveland, Ohio were married. They had two children named Max and Francis.
Jenney was elected an Associate of the American Institute of Architects in 1872, and became a Fellow in 1885. He served as first Vice President from 1898 to 1899. He died in Los Angeles, California, on June 14, 1907. After Jenney's death, his ashes were scattered over his wife's grave, just south of the Eternal Silence section of Uptown's Graceland Cemetery.