St. Paul's School for Boys was founded in 1849 as an Episcopal school for poor boys at Old St. Paul's Parish in Baltimore City by the Reverend William Edward Wyatt.

St. Paul's moved its campus four times until relocating at the current grounds in 1952. The principal administrative building on campus is Brooklandwood, a mansion built in 1793 by Charles Carroll of Carrollton (1737-1832), one of the signers of the Declaration of Independence.

At the time of the school's founding in the mid-nineteenth century, boys studied Greek, Latin, and math. Church music was also given high priority, and the choral music program continues to thrive. Today St. Paul's School for Boys offers a college-preparatory curriculum and students can pursue the International Baccalaureate (IB) Diploma Program.

St. Paul’s School for Girls traces its roots to 1799 when the Benevolent Society of Baltimore, founded by a group of parishioners from Old St. Paul's Church, established an institution for the care and education of indigent or orphaned girls.

During the 1800s and 1900s, the school closed and reopened several times with different names and in different locations. In 1958, members of the Benevolent Society voted to establish a new college-preparatory school, which opened officially in 1959 on a site adjacent to St. Paul's School for Boys.

The girls’ school's signature academic programs include SPIRITUS Scholars, a two-year research program for juniors and seniors, and the Real-World Experiences career exploration program.

St. Paul's School for Girls shares a campus with St. Paul's School for Boys and with St. Paul's Pre and Lower School (coed). In July 2018, the schools unified under the umbrella of The St. Paul's Schools, with a single board of trustees and one president.