Hamilton, an Irish emigrant, lived in Lawrenceburg in Dearborn County, Indiana in 1820, when he married Emerine J. Holman, the daughter of a prominent Indiana judge. In 1823 the Hamilton family moved to Fort Wayne, where Hamilton was appointed deputy clerk in the U. S. Land Office. Hamilton also served as Allen County sheriff (1824–1826), Fort Wayne’s postmaster (1825–1831), and as Allen County auditor, clerk, and recorder (1831–1838).
In the 1820s Hamilton partnered with Cyrus Taber to form Hamilton and Taber, an Indian trading company. The firm prospered as Hamilton won the trust and confidence of many Indians, in particular Chief Jean Baptiste de Richardville of the Miami. In 1834 and 1838 Hamilton was appointed to the U. S. Commission to Negotiate Treaties with the Miami in northern Indiana. In 1840 he served on the Commission to Extinguish Indian Titles in Indiana and was appointed the U. S. Indian agent to the Miami from 1841 to 1845. Hamilton was a Whig delegate to the Indiana Constitutional Convention in 1851 and was elected to the Indiana Senate in 1859, serving one term.
Until his death in 1864 Hamilton remained active in business as president of the Fort Wayne branch of the Indiana State Bank and of the Allen Hamilton National Bank in Fort Wayne. He resided at "Veraestau" and is buried in Lindenwood Cemetery.
In 1861 Hamilton donated land for a baseball field at the corner of Lewis Street and Calhoun Street in Fort Wayne, the site of the first professional league baseball game played in 1871 for the National Association of Professional Baseball Players. The Fort Wayne Kekiongas won the game.
Hamilton was the grandfather of author Edith Hamilton, whose books on mythology have become classics, and Alice Hamilton, a pioneer in American industrial medicine and the first woman on the Harvard University medical faculty. His great-grandson, Holman Hamilton, is noteworthy for a two-volume biography of President Zachary Taylor.
- "Historical Sketch" in "Allen Hamilton Papers, 1814-1924, Collection Guide" (PDF). Indiana Historical Society. 1992. Retrieved 2012-10-22.
- Judge Jesse Holman was a justice of the Indiana Supreme Court and a founder of Indiana University, Franklin College, and the Indiana Historical Society. Gugin and St. Clair, Justices of the Indiana Supreme Court, p. 9.
- "Indiana State Historic Architectural and Archaeological Research Database (SHAARD)" (Searchable database). Department of Natural Resources, Division of Historic Preservation and Archaeology. Retrieved 2015-07-01. Note: This includes Arthur L. Paulison (n.d.). "National Register of Historic Places Inventory Nomination Form: Lindenwood Cemetery" (PDF). Retrieved 2015-07-01. and Accompanying photographs
- Brice, Wallace. History of Fort Wayne. Fort Wayne, IN: D. W. Jones and Son, 1868.
- Gugin, Linda C., and James E. St. Clair, eds. Justices of the Indiana Supreme Court. Indianapolis, IN: Indiana Historical Society Press, 2010. ISBN 9780871952882 WorldCat
- Hamilton, Allen, Papers, 1814–1924. “Collection Guide.” William Henry Smith Memorial Library, Indiana Historical Society, Indianapolis, IN. Retrieved February 6, 2012.