[3] Brown played an important role in controlling the Pratt Street Riot, where the first bloodshed of the Civil War occurred, on April 19, 1861.

When the column he was leading was assailed by the mob, "the mayor's patience was soon exhausted, and he seized a musket from the hands of one of the men and killed a man therewith.

"[4] Immediately following the Riot, Baltimore saw much lawlessness, as citizens destroyed the offices of pro-Union German newspapers and looted shops in search of guns and other weapons.

In the few days following the Pratt Street Riot, Governor Hicks likely assented to Mayor Brown's decision to dispatch the Maryland militiamen to destroy the railroad bridges over the rivers north of the city, to prevent more troops from passing through Baltimore.

While speaking at St. John's College in Annapolis, MD, in 1869, Brown made reference to “A great university hereafter to be established in Baltimore … planned … by the wealthiest of her citizens, a native of this county [ Anne Arundel County ].” While Brown did not name the individual, he was referring to Johns Hopkins, who in 1867 had announced his intention to found a university and a hospital upon his death.

[citation needed] After Hopkins’ death on December 24, 1873, and the settling of his estate, the trustees began in earnest to plan the new university.

[citation needed] Brown offered his own ideas, one of which was that the university should send into the world “upright, refined, and highly cultivated young men.” He also declared that the aim of the new university should be “to bring together a competent corps of professors, some of whom, if possible, should be teachers in the largest sense, that is, should have the ability and the leisure too, to add something by their writings and discoveries to the world’s stock of literature and science….”[6] This idea was paraphrased and endorsed by President Gilman in his Inaugural Address delivered on February 22, 1876.

In it, he referred to Quaker Johns Hopkins as a "wealthy Union man" and a member of a committee of bankers who gave $500,000 to the city of Baltimore after the first blood in the Civil War was shed there.