Warner was born of Puritan descent in Plainfield, Massachusetts. From age six to age fourteen, he lived in Charlemont, Massachusetts, the scene of the experiences pictured in his study of childhood, Being a Boy (1877). He then moved to Cazenovia, New York, and in 1851 graduated from Hamilton College, Clinton, NY.

He worked with a surveying party in Missouri; studied law at the University of Pennsylvania; practised in Chicago (1856–1860); was assistant editor (1860) and editor (1861–1867) of The Hartford Press, and after The Press was merged into The Hartford Courant, was co-editor with Joseph R Hawley; in 1884 he joined the editorial staff of Harper's Magazine, for which he conducted The Editors Drawer until 1892, when he took charge of The Editor's Study. He died in Hartford on October 20, 1900, and was interred at Cedar Hill Cemetery, with Mark Twain as a pall bearer and Joseph Twichell officiating.

He travelled widely, lectured frequently, and was actively interested in prison reform, city park supervision, and other movements for the public good. He was the first president of the National Institute of Arts and Letters, and, at the time of his death, was president of the American Social Science Association. He first attracted attention by the reflective sketches entitled My Summer in a Garden (1870; first published in The Hartford Courant), popular for their abounding and refined humour and mellow personal charm, their wholesome love of outdoor things, their suggestive comment on life and affairs, and their delicately finished style, qualities that suggest the work of Washington Irving. He is now best known for making the remark "Everybody complains about the weather, but nobody does anything about it". This was quoted by Mark Twain in a lecture, and is often attributed to him.

• Saunterings (descriptions of travel in eastern Europe, 1872)
• BackLog Studies (1872)
• Baddeck, and That Sort of Thing (1874), travels in Nova Scotia and elsewhere
• My Winter on the Nile (1876)
• In the Levant (1876)
• In the Wilderness (1878)
• A Roundabout Journey, in Europe (1883)
• On Horseback, in the Southern States (1888)
• Studies in the South and West, with Comments on Canada (1889)
• Our Italy, southern California (1891)
• The Relation of Literature to Life (1896)
• The People for Whom Shakespeare Wrote (1897)
• Fashions in Literature (1902)

He also edited The American Men of Letters series, to which he contributed an excellent biography of Washington Irving (1881), and edited a large Library of the World's Best Literature.

His other works include his essays:

• As We Were Saying (1891)
• As We Go (1893)

And his novels:

• A Tale of Today (in collaboration with Mark Twain, 1873)
• Their Pilgrimage (1886)
• A Little Journey in the World (1889)
• The Golden House (1894)
• That Fortune (1889).

See the biographical sketch by TR Lounsbury in the Complete Writings (15 vols, Hartford, 1904) of Warner.