The region around Auburn had been Haudenosaunee territory for centuries before European contact and historical records.
Auburn was founded in 1793, during the post-Revolutionary period of settlement of western New York. The founder, John L. Hardenbergh, was a veteran of the Sullivan-Clinton campaign against the Iroquois during the American Revolution. Hardenbergh settled in the vicinity of the Owasco River with his infant daughter and two African-American indentured servants, Harry and Kate Freeman. After his death in 1806, Hardenbergh was buried in Auburn's North Street Cemetery, and was re-interred in 1852 in Fort Hill Cemetery – the first burial in the city's newly opened burial ground. The community grew up around Hardenbergh's gristmill and sawmill.
Originally known as Hardenbergh's Corners in the town of Aurelius, the settlement was renamed Auburn in 1805 when it became the county seat. It became an incorporated village in 1815, and was chartered as a city in 1848. It was only a few miles from the Erie Canal, which opened in 1825 and allowed local factories to inexpensively ship goods north or south. In 1871, the Southern Central Railroad, financed by the Lehigh Valley Railroad, completed a line primarily to carry coal from Athens, Pennsylvania, through Auburn to wharves on Lake Ontario at Fair Haven.