The town of Lima was organized in 1789 (before Livingston County was established) as the "Town of Charleston," but was renamed "Lima" in 1808 to reflect that many residents had come from Old Lyme, Connecticut and to avoid confusion with Charleston, New York.
The Genesee Wesleyan Seminary (1830) / Genesee College (1849) in Lima village was one of the first co-educational schools in the country when it first opened in 1822. Eventually, determined by a Methodist-Episcopal convention in 1870, the college was shut in favor of the newly developed Syracuse University (1871), over the protests of the residents of Lima. The campus is now home to Elim Bible Institute.
The population of Lima was 1,890 in 1920.
The Ganoung Cobblestone Farmhouse, Godfrey House and Barn Complex, Leech-Lloyd Farmhouse and Barn Complex, Leech-Parker Farmhouse, Markham Cobblestone Farmhouse and Barn Complex, Martin Farm Complex, Ogilvie Moses Farmhouse, Zebulon Moses Farm Complex, and Thomas Peck Farmhouse are listed on the National Register of Historic Places.