[3] During the Civil War, Van Brunt served as Secretary to the Admiral of the North Atlantic Squadron, United States Navy.

The firm produced designs for many buildings in the Boston area, including Harvard University's Memorial Hall, "said to be one of the greatest examples of Ruskinian Gothic architecture outside of England".

In 1874 Van Brunt published a translation of Eugène Viollet-le-Duc's Discourses on architecture, and he remained a prolific writer through his career.

The same year, Van Brunt and former employee Frank M. Howe established the firm of Van Brunt & Howe, and about six years after took the dramatic step of moving his office from Boston to Kansas City,[6][7] partly for multiple commissions for the Union Pacific Railroad for grand stations in western cities like Ogden, Utah (1889; burned down 1923), Denver, Colorado (1895; rebuilt 1912), Cheyenne, Wyoming and Omaha, Nebraska (1899; replaced 1931).

Stylistically, most of his later work is comfortably consistent with Richardsonian Romanesque; in at least one case, the Hoyt Library, he adapted and finished a rejected Richardson design.