Clifton is at the junction of State Highway 6 and Farm Road 219, thirty-five miles northwest of Waco in southern Bosque County. It was founded in the winter of 1852–53, when the families of Samuel Locker, Monroe Locker, Frank Kell, and T. A. McSpadden settled in the vicinity. The town was named Cliff Town after the limestone cliffs that surround it. Over the years the name was altered to Clifton. The site was originally on the banks of Clear Branch. The Masonic hall and a log schoolhouse were the first public buildings. The post office was established in 1859. The First Presbyterian Church of Clifton was organized in 1861 and is the oldest church in continuous service in the county. The Baptists built the first church building in Clifton in 1884–85. After the Civil War J. Stinnett built a flour mill that was powered by the Bosque River. It was replaced in 1868 by a limestone mill, which was eventually converted to the electric power plant that provided the first electricity for Clifton homes. A three-story school known as Rock School was built around 1870 and served the community for more than twenty years. In 1893 a new building was constructed on property donated to the Clifton school system.
In 1880 the Gulf, Colorado and Santa Fe Railway built a station a mile south of Clifton. Merchants moved their businesses closer to the railroad station, and the town thrived as a business and trade center. The Merchant Exchange and Flour Mill, the first steam flour mill in the Bosque valley, was established in 1887 or 1888. The Clifton Record, a newspaper that began publishing in 1895 under the ownership of W. C. O'Brian, continued to serve the community through the years. Clifton also served as the county seat between 1890 and 1892. Clifton Lutheran College, later known as Clifton College, opened in 1896. The community was incorporated in 1901. An earlier attempt at incorporation in 1891 failed when the election results were declared invalid. A fire on December 23, 1906, destroyed a large portion of the business district, which was eventually rebuilt. The Clifton Volunteer Fire Department was organized in 1907. The town's need for a hospital was met by Dr. V. D. Goodall and Dr. S. L. Witcher in 1938. The Lutheran Sunset Home for the elderly was established in Clifton in 1954. The town had an estimated population of 204 in 1904 and 3,195 in 1990. It had 100 businesses in the 1980s. In the early 1990s an exotic-animal preserve open to tourists was located southwest of Clifton on Farm Road 3220. In 2000 the population was 3,542 with 262 businesses.