Samuel Pearson, the mill's founder, is thought to have first acquired property in the Wake County area around 1750, when he purchased land from John Monk. The earliest known document related to Pearson's activity around Steep Hill Creek and the land that now surrounds the mill dates to 1756. This document, a request for a land survey, appears to include the land where Samuel's home stood. After this 1756 request, Samuel Pearson officially received the related land grant in 1761. In March 1763, Pearson submitted an entry, claiming ownership of the land where he built the mill. No subsequent documents were issued regarding this piece of land because the British land office ceased operation after the Earl of Granville's death later that year. The start of the American Revolution several years later further delayed the issuance of new land. Action was not taken until 1778, when the new State of North Carolina issued Pearson a survey for the same land he claimed in 1763. This survey is the first known document on file that specifically mentions the mill as already standing.

Samuel Pearson owned the mill until his death in 1802. In his will, he divided his land among his four sons, and intended the proceeds of the sale of his personal property to go to his six daughters. His son, Simon Pearson, received 340 acres of land that included the old mill. Because of debts owed to the State Bank of North Carolina, Simon Pearson was forced to sell his land, including the mill, in a sheriff's sale in 1819.

The sheriff sold the property for $3,031 to William Boylan, a prominent Raleigh businessman and director of the State Bank. Boylan established Raleigh's first newspaper, The Raleigh Minerva, by the close of the 19th century; he later also established the Raleigh Advertiser. He also served on the commission to build a new state capital. In order for the mill to continue as a successful business, Boylan made constant changes to the mill building and its operation. Architectural evidence shows that major renovations were likely made to the structure between 1820 and 1850. This most likely came in response to a flood in the early 1800s, which probably destroyed the original mill; however, despite that setback, Boylan had a sawmill operating at the mill by the 1840s.

Mr. Boylan owned the mill for 37 years. He sold it to John Primrose, Thomas H. Briggs and James Penny on June 30, 1853. In 1859, James Dodd bought Primrose’s share of the mill. Thomas H. Briggs was a prosperous Raleigh businessman who started a building materials business that continues today as Briggs Hardware. Briggs was Raleigh’s most influential post-Civil War businessman. Having converted his Confederate currency into silver before the war’s conclusion, Briggs was one of the few North Carolinians with money to invest during Reconstruction.

On March 2, 1863, Penny, Dodd and Briggs sold the mill and 94 surrounding acres to Phares Yates. James Penny’s possible involvement in the murder of Hinton Franklin may have prompted the sale. Local legend says Franklin was a northern sympathizer whom Penny reportedly killed for not paying a $700 mill debt. Franklin's widow supposedly told Union troops that were occupying the Raleigh area in 1865 that her husband’s death was a result of his political beliefs. Allegedly, the troops tried to burn the mill by setting fire to the entrance porch. Charred wooden beams from the mill’s underside are possible evidence of the attempted burn. Court records show that Penny was tried for murder in December 1866 but was found not guilty.

Ten years later, Minnie Yates and her son Wilbur sold the mill to the Trojan Sales Company, a subsidiary of A.E. Finley Associates. The title was later transferred to the North Carolina Equipment Company, another subsidiary of A.E. Finley Associates. A.E. Finley built a retreat lodge for use by his family and employees on the millpond. The mill continued operation until the 1950s, when it closed for lack of business.

North Carolina State University obtained title to the mill and the pond in 1963. The property was part of a 1,000-acre tract that was purchased for use by North Carolina State University Field Laboratory’s experimental farms and demonstration fields. Shortly after the University obtained the property, John Daniel Lea – the miller who had worked at the mill since 1898 – operated the mill for the last time as a demonstration.

In 2001 N.C. State leased 158 acres to Wake County. In addition, Wake County bought 16 acres upstream and signed a memorandum of understanding with the N.C. Department of Agriculture for the development of hiking trails on 400 acres of land upstream from the pond. Shortly after park planning began, Hurricane Fran breached the dam, drained the millpond and caused the shed to collapse in the fall of 1996. The mill and its pond were badly damaged, but not beyond repair. Restoration of the mill and its grinding machinery was finally finished in 2005.

Construction of the visitor center for the park began in summer 2003, and was completed in April 2006. Historic Yates Mill County Park opened to the public May 20, 2006. Tours of Yates Mill are available to the public March through November, and corn-grinding demonstrations are offered the third weekend of each month during that time.