Lincoln Township was surveyed in October and November 1848 and May 1849 by government surveyors Andrew Leach, James M. Marsh and Edwin James, Jr. Twelve Mile and Three Mile rivers cross diagonally near the center of the township.
Like other parts of the county the prairie lands were not settled up for nearly twenty years after early location had been made in the groves and timber. The first permanent settler, R. M. Thompson came from Monroe County, Iowa in 1853 to locate on section 25. He built a log house on timber near the head of a branch of Three Mile River.
The next season brought in settlers Henry Rose, James Thompson, Benjamin Thompson, J. M. Thompson, William Peck Peter Rouser, W. B. Lewis and Hamilton Wheeler. These settlers were joined in 1855 by B. D. Bilbo, Isaac Crist and William Wickham. S. L. Emerson came from Ohio, purchased land adjoining the county farm, built a log cabin and brought his wife and two children to live in 1856.
The township was organized by order of Judge J. W. McDill on 08 October 1860. The first election was held on 06 November 1860. Elected to township offices were as follows; School board directors, S. L. Emerson, president; William Peck, secretary; Reuben Abbott, treasurer; County supervisor, C. G. Roberts; Justice of the peace, S. L. Emerson; Township trustees, B. D. Bilbo, Joseph Thompson and R. A. Abbott; Township clerk, William Peck; Assessor, W. M. Wickham; Constables, J. M. Thompson and Jacob McKnight; Road supervisor, R. M. Thompson.
However, not until 06 September 1870 it was resolved by the board of supervisors of Union County at the courthouse in Afton, that the township be set off as a civil township with the name, Lincoln. With that action, the size of the township was reduced to the present day size.
In response to the call of the president on 14 April 1861 for volunteer soldiers to suppress the rebellion, more than one-half of the able bodied men of the township enlisted. B. D. Bilbo was killed in battle, J. H. Deuel and R. M. Thompson died in the service and a number were wounded. Most of those who were able, re-enlisted and served to the end of the war.
Lincoln Township had one post office from 1881 to 1885 by the name of Lee. Information from 1908 Union County History by George A Ide.
Lincoln Township has two cemeteries, Old Jerusalem Cemetery and Evergreen Cemetery also know as Jerusalem Cemetery.