The revelation by the university, which boasts a long tradition of inclusion, comes as the United States continues reckoning with its own history of racism after widespread protests against discrimination earlier this year.
Calls to dismantle statues of leaders from the historic slave-owning South have multiplied, and the legacies of some of America's "founding fathers" such as George Washington and Thomas Jefferson, also slave owners, have been reassessed.
"We have for almost 100 years communicated a story about our origins which is not correct," Johns Hopkins University president Ron Daniels said Friday in a Zoom discussion.
"The revelation of this part of Mr Hopkins' life is devastating," he added.
Hopkins came from a wealthy Maryland family and made his fortune in commerce and banking.
Raised in the Quaker faith, a Protestant movement opposed to slavery, he supported President Abraham Lincoln during the Civil War.
When he died in 1873, he bequeathed part of his fortune for the creation of an orphanage for Black children, a university and a hospital where all patients would be accepted regardless of gender or origin.
But according to census records discovered this summer and dating from 1840 and 1850, Hopkins owned slaves -- one in 1840, and then four a decade later.
There is no indication that he ever freed them.
The revelations are a shock for the elite private university founded in his name in 1876, and which has championed diversity from its base in the Maryland city with a predominantly Black population beset by poverty.
Little remains of Johns Hopkins and his family. Much of his story is based on glowing newspaper articles published after his death and on the memoirs of his great-niece, Helen Hopkins Thom, which date from 1929.
The work of finding the truth has only just begun, said Martha Jones, head of the university's commission to try to find the descendants of these unknown slaves.
"We are at the beginning of dismantling what it turns out were foundational myths about the origins of not only Mr Hopkins' own life, but the trajectory of his life and ultimately the gift that he makes that establishes this institution," she said.
