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Fisk Brewer's parents were missionaries to the Greeks of Asia Minor, who came fro distinguished families. Brewer’s three uncles were Stephen Johnson Field (1816-99), associate justice of the U.S. Supreme Court (1863-97), Donald Dudley Field (1805-94), an attorney known for the “Field Code” of civil procedure, and Cyrus West Field (1819-92), a financier responsible for laying the first transatlantic cable. Fisk’s brother, David Josiah Brewer (1837-1910), was also an Associate Justice of the U.S. Supreme Court (1889-1910). Brewer was named for two missionary friends of his parents: Pliny Fisk (1792-1825) and Levi Parsons (1792-1822). His parents came from old New England families and were ardent Abolitionists. After returning to his ancestral Connecticut in 1858, Brewer spent his early childhood inHartford and New Haven and was later schooled in Massachusetts and Connecticut before graduating from Yale, where he twice won the Greek prize and developed a lifelong interest in numismatics, which became the focus of his major publications.  He tutored at Beloit and Yale, where he catalogued the college's numismatic collection. He then spent a year in Greece studying modern Greek and archaeology. His familiarity with the language and the landscape served him well in later years during his consulship, served largely in the Piraeus. Upon his return to America, he married Julia Richards, herself the daughter of missionaries to Hawaii. 

Less than a year after his marriage, he was diagnosed with a form of tuberculosis called "slow consumption" and was advised by his doctors to move south for his health. When the Civil War ended, he worked with the American Union Commission, constituted to aid people impoverished by the war and to regain their civil and racial rights, he agreed to lead the all-black Freedmen's School in Raleigh, then the North Carolina School for the Deaf, Dumb and Blind. He wrote, "The black boy...who has learned the long paradigms of Greek and Latin, and read in the original of Caesar's wars and of Xenophon's march, Cicero's patriotic orations and the poetry of Virgil and Homer—is no longer a cornfield negro. He has a platform of common knowledge and sentiment with his white classmate. Either there is no virtue in the humanities, or he has acquired something of true courtesy." The radical president of the University of North Carolina, Solomon Pool (1832-1901), reorganized the university in 1869, and Brewer signed on as librarian and professor of Greek, in part because Pool favored integration of the campus, which led to a boycott by whites and the university was obliged to close from 1871 to 1875 for lack of students. When the university closed,Brewer became a charter member of the APA in 1869. He greatly expanded the university library, but also suffered abuse from whites as a New England abolitionist who socialized with blacks. The University was closed from 1871-5, during which time President U.S. Grant named him consul to Greece. There he was able to enlarge his study of Greek and visit the great sites. Upon his return in 1873, he took a position at the University of South Carolina, then the first integrated college of the Old South, as professor of ancient languages and secretary pro tem of the faculty. The first African American hired by the university, Richard T. Greener (1844-1922), the first African-American graduate of Harvard, was hired in the same year as professor of mental and moral philosophy, but he also served as librarian and taught Greek. Brewer had been a founding ember of the American Philological Association in 1869 and gave ten papers at early meetings. in 1875 he nominated Greener for membership. Greener was accepted and became the first member of the APA of African American descent. Brewer found a Latin manuscript in the University's collections which he deciphered and shared with Greener, The manuscript was the basis of Greener's paper to be delivered at the 1877 APA meeting in Baltimore. 

The end of Reconstruction in 1877 found Greener and Brewer fearing for their lives. The University closed in that year and Greener went on to a productive career that saw hi ultimately become dean of Howard University Law School. Brewer moved to Iowa College, whose campus and buildings he navigated in a wheelchair until his illness forced him to retire. Bedridden for the last decade of his life, he nevertheless read and gathered examples for Liddell and Scott's Greek dictionary, and even contributed to TAPA, until tuberculosis took his life at the age of 57.