The community was founded in 1879 by James W. Webster under the name "Gardentown". It was established initially as a colony for settlers from England. It began as a stopover for travelers between Houston/Harrisburg, Galveston, Kemah, and Seabrook. Eventually railroads, such as the Missouri, Kansas and Texas Railway, were built through the area. Farmers in the area raised pears and other produce.

In 1903, the Houston Chamber of Commerce invited Seito Saibara, a former Japanese member of parliament and a Christian theologian, to come to Texas to teach rice farming. Rice at that time was emerging as an important cash crop. Saibara settled in Webster and established a small farming community of Japanese Christians. Saibara and his son Kiyoaki established the foundations of what became the rice industry of the U.S. Gulf Coast.

Dairies and livestock ranches developed in the town as well in the early 1900s. Petroleum was discovered at the Webster-Friendswood Oilfield in the 1930s, but the population remained small. The community was incorporated in 1958.

In 1961 the National Aeronautics and Space Administration announced that it was building the Manned Spacecraft Center (now known as the Johnson Space Center) nearby along the shores of Clear Lake. Growth and development quickly swept over the Clear Lake Area, and Webster's population blossomed. Webster today has become a thriving bedroom community closely tied to the Clear Lake Area and its high-tech industry.