From 1856 to 1865 Gilman served as librarian of Yale College, and was also concerned with improving the New Haven public school system.
When the Civil War broke out, Gilman became the recruiting sergeant for the Norton Cadets, a group of Yale graduates and faculty who drilled on the New Haven Green under the oversight of Yale professor William Augustus Norton.
In 1863, Gilman was appointed professor of geography at the Sheffield Scientific School, and became secretary and librarian as well in 1866.
Having been passed over for the presidency of Yale, for which post Gilman was said to have been the favorite of the younger faculty, he resigned these posts in 1872 to become the third president of the newly organized University of California, Berkeley.
His work there was hampered by the state legislature, and in 1875 Gilman accepted the offer to establish and become first president of Johns Hopkins University.

Before being formally installed as president in 1876, he spent a year studying university organization and selecting an outstanding staff of teachers and scholars.
His formal inauguration, on 22 February 1876, has become Hopkins' Commemoration Day, the day on which many university presidents have chosen to be installed in office.
Among the legendary educators he assembled to teach at Johns Hopkins were classicist Basil Lanneau Gildersleeve, mathematician James Joseph Sylvester, historian Herbert Baxter Adams and chemist Ira Remsen.

Gilman's primary interest was in fostering advanced instruction and research, and as president he developed the first American graduate university in the German tradition.
The aim of the modern research university, said Gilman, was to "extend, even by minute accretions, the realm of knowledge" At his inaugural address at Hopkins, Gilman asked: "What are we aiming at?"
The answer, he said, was "the encouragement of research and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell."

In 1884, Gilman was elected a member of the American Antiquarian Society.

Gilman was also active in founding Johns Hopkins Hospital (1889) and Johns Hopkins Medical School (1893).
He founded and was for many years president of the Charity Organization of Baltimore, and in 1897 he served on the commission to draft a new charter for Baltimore.
From 1896 to 1897, he was a member of the commission to settle the boundary line between Venezuela and British Guiana.

Gilman served as a trustee of the John F. Slater and Peabody education funds and as a member of John D. Rockefeller's General Education Board.
In this capacity, he became active in the promotion of education in the southern United States.
He was also president of the National Civil Service Reform League (1901–1907) and the American Oriental Society (1893–1906), vice president of the Archaeological Institute of America, and executive officer of the Maryland Geological Survey.
He retired from Johns Hopkins in 1901, but accepted the presidency (1902–1904) of the newly founded Carnegie Institution of Washington.

His books include biographies of James Monroe (1883) and James Dwight Dana, a collection of addresses entitled University Problems (1898), and The Launching of a University (1906).
From 1856 to 1865 Gilman served as librarian of Yale College, and was also concerned with improving the New Haven public school system. When the Civil War broke out, Gilman became the recruiting sergeant for the Norton Cadets, a group of Yale graduates and faculty who drilled on the New Haven Green under the oversight of Yale professor William Augustus Norton. In 1863, Gilman was appointed professor of geography at the Sheffield Scientific School, and became secretary and librarian as well in 1866. Having been passed over for the presidency of Yale, for which post Gilman was said to have been the favorite of the younger faculty, he resigned these posts in 1872 to become the third president of the newly organized University of California, Berkeley. His work there was hampered by the state legislature, and in 1875 Gilman accepted the offer to establish and become first president of Johns Hopkins University.
Before being formally installed as president in 1876, he spent a year studying university organization and selecting an outstanding staff of teachers and scholars. His formal inauguration, on 22 February 1876, has become Hopkins' Commemoration Day, the day on which many university presidents have chosen to be installed in office. Among the legendary educators he assembled to teach at Johns Hopkins were classicist Basil Lanneau Gildersleeve, mathematician James Joseph Sylvester, historian Herbert Baxter Adams and chemist Ira Remsen.
Gilman's primary interest was in fostering advanced instruction and research, and as president he developed the first American graduate university in the German tradition. The aim of the modern research university, said Gilman, was to "extend, even by minute accretions, the realm of knowledge" At his inaugural address at Hopkins, Gilman asked: "What are we aiming at?" The answer, he said, was "the encouragement of research and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell."
In 1884, Gilman was elected a member of the American Antiquarian Society.
Gilman was also active in founding Johns Hopkins Hospital (1889) and Johns Hopkins Medical School (1893). He founded and was for many years president of the Charity Organization of Baltimore, and in 1897 he served on the commission to draft a new charter for Baltimore. From 1896 to 1897, he was a member of the commission to settle the boundary line between Venezuela and British Guiana.
Gilman served as a trustee of the John F. Slater and Peabody education funds and as a member of John D. Rockefeller's General Education Board. In this capacity, he became active in the promotion of education in the southern United States. He was also president of the National Civil Service Reform League (1901–1907) and the American Oriental Society (1893–1906), vice president of the Archaeological Institute of America, and executive officer of the Maryland Geological Survey. He retired from Johns Hopkins in 1901, but accepted the presidency (1902–1904) of the newly founded Carnegie Institution of Washington.
His books include biographies of James Monroe (1883) and James Dwight Dana, a collection of addresses entitled University Problems (1898), and The Launching of a University (1906).
Daniel Coit Gilman