Although he did not participate in his father's raid on Harpers Ferry, Virginia, he served as his intelligence agent and liaison.

John Jr. described the trip as "a horrid business in a low stage of water which is a considerable portion of the year."

Most of the passengers and crew were pro-slavery, and the captain deliberately left the two brothers' parties behind at a stop in Waverly, Missouri.

However, he was captured by Henry Clay Pate, a border ruffian and commander of a proslavery militia, in connection with the murders.

His father took his son's heavy chains and padlocks first to Concord to show to "Emerson and his friends", and then he held them up at antislavery meetings in different places.

Kansapedia says that when the time came to make a decision on participation, "Brown, who was suffering from mental illness, experienced more anxiety.

In the early summer of 1859 John travelled around what is today Ontario, Canada (Hamilton, St. Catharines, Chatham, London, Buxton, and Windsor), seeking support from Canadian negroes for his father's project.

[12] The letter told John Jr. to do this "with perfect quiet" and to move only the tools, "not the other stuff", to a safe place where only Jr. and "the keeper" would know where they were.

[12] When his brother Owen escaped capture, he took safe refuge with John Jr. at this home in northeast Ohio.

A deputy of the Senate's Sergeant-at-Arms was sent to arrest the individuals—according to the report, Brown was then living in Ashtabula County, Ohio—and bring them to Washington.

[14] In the summer of 1860, John Jr. was an agent of the "Haytian Bureau of Emigration", working under his father's former associate and biographer James Redpath.

His intention was to enlist "abolitionists of the intense sort"[17] and muster them under Colonel James Montgomery, one of Lane's three Lieutenants.

[18] In August he wrote to Gerrit Smith from Jefferson, Ashtabula County, Ohio, returning to him the land he had been given in North Elba.

[19] John Brown's "Sharpshooters" garnered significant press attention as they traveled from Ohio to Kansas.

[17][22] But according to John Jr., “Before our regiment left Missouri more than two thousand slaves were by us restored to the possession of themselves, were ‘Jayhawked’ into freedom.

"[23] He was succeeded as captain of the company by his second lieutenant, George H. Hoyt, who had been one of his father's lawyers following the Harpers Ferry attack.

In contrast with his brother Owen, he "delights to tell the tragic story of his father's life to intimate acquaintances".

"[41] "His family and himself are beloved and sympathized with by his neighbors of all parties; and well he may be; for he is one of the finest specimens of men, physically and intellectually.

"[42] Brown's visitor about 1871 described him as a "quiet, genial, warm-hearted farmer, amateur geologist, and land surveyor";[43] a later one as "sunny, cheery-voiced", with "fine manners and an easy address".