After service for the Confederate States Army in the American Civil War, during which Gildersleeve was shot in the leg, he returned to the University of Virginia.

[4] Ten years later, he accepted an offer from Daniel Coit Gilman to teach at Johns Hopkins University in Baltimore.

[5] When the Johns Hopkins University opened in 1876, Gildersleeve was one of five original full professors and was responsible for setting up a program in the study of Greek and Roman literature, at which he succeeded admirably.

Johns Hopkins was known to be opposed to slavery, founding president Daniel Coit Gilman was from Connecticut, and most other faculty were from the northern states, which led to suspicion regarding the intent of the new institution.

His special interest in Christian Greek was partly the cause of his editing the Apologies of Justin Martyr (1877), which claimed to have "used unblushingly as a repository for [his] syntactical formulae."

Gildersleeve's studies under Franz had no doubt quickened his interest in Greek syntax, and his logic, untrammeled by previous categories, and his marvelous sympathy with the language were displayed in this most unlikely of places.

His views on the function of grammar were summarized in a paper on The Spiritual Rights of Minute Research delivered at Bryn Mawr on June 16, 1895.

[3] The Atlantic Monthly published an article by Gildersleeve titled "The Creed of the Old South" in January 1892, and an essay, "A Southerner in the Peloponnesian War", in September 1897.

In a memorial published in the American Journal of Philology, Professor C. W. E. Miller paid tribute to Gildersleeve, stating, "Of Greek authors, there were few with whom he did not have more than a bowing acquaintance.

In Soldier and Scholar: Basil Lanneau Gildersleeve and the American Civil War, Ward Briggs published editorials written by Gildersleeve while he served as a staff officer in the Confederate Army and as a professor at the University of Virginia, which feature vitriolic attacks on critics of slavery with parallels drawn to ancient Greek authors and situations.