Huchra, who was born in Jersey City, New Jersey, was educated at the Massachusetts Institute of Technology and the California Institute of Technology, where he obtained his PhD in 1976. He then moved to Harvard serving as professor of astronomy, and as a staff member at the Smithsonian Astrophysical Observatory. He moved to Harvard in 2005.

In the early 1980s Huchra worked on the Tully-Fisher relation, which links the intrinsic luminosity of a spiral galaxy with the rotational velocity of its stars. He found that with regard to galaxies in the Coma cluster there was a departure of up to 20% from the supposed correlation. Huchra went on in 1982 with a number of colleagues to apply the relation to the Local Group of galaxies to see if the peculiar motion tentatively identified by Vera Rubincould be detected. The peculiar velocities of several hundred galaxies in the region of the Virgo cluster were measured. They found that velocities in the direction of Virgo steadily increased, while decreasing on the other side. The result has been interpreted by some as evidence for the existence of The Great Attractor, a proposed massive concentration of galaxies lying beyond the Hydra-Centaurus supercluster.

In 1986 in collaboration with Margaret Geller, Huchra began a galactic survey for the Smithsonian Center for Astrophysics (CfA). They used a 1.5-meter telescope located on Mount Hopkins, Tucson, Arizona and sought to measure the red shifts of galaxies below a magnitude of 15.5 and falling within a wedge of sky 6° wide, 120° long, and out to a distance of about 300 million light years. By 1989 they had mapped the positions of 10,000 galaxies.

To their surprise, instead of producing a uniform distribution their maps revealed large voids within which huge clusters of galaxies were distributed. The largest structure they observed, dubbed The Great Wall, stretched 500 million light years without its edge being found.