Huntsville, Texas was founded by Pleasant and Ephraim Gray in either 1835 or 1836. It was originally an Indian trading post and was named after Huntsville, Alabama, where the Gray family had previously resided. When Walker County was organized in 1846, Huntsville was named its county seat. From all appearances, the relationship between Huntsville and the local Native Americans, the Bidai, the Alabama and Coushatta, was a peaceful one.

The river port town of Cincinnati, Texas, located about twenty miles north of Huntsville, provided access to the Trinity River. This was a boon to the local businesses in Huntsville. As business grew, Huntsville grew. Many newcomers relocated to Huntsville to make their money in the timber industry.

At some point in the early 1840s, the Brick Academy was founded. It was a male and female school sometimes called the Huntsville Male and Female Academy. In the fall of 1845, the Stovall Male and Female Academy began. It later dropped females from its student body and accepted only males. It became Huntsville Male Institute in 1848. The Methodist established the Andrew Female College in the early 1850s. It was finally abandoned when Sam Houston Normal Institute, a teacher training college was established. It later became Sam Houston University. In 1847 Huntsville was selected to became the site of the new Texas State Penitentiary. On October 1, 1849, it welcomed its first inmate.

In the early 1850s, Austin College opened in Huntsville. It later relocated to Sherman, Texas in 1877, at which time the Methodist Church bought the property to house a boys school, Mitchell College.

During the Civil War, citizens of the Huntsville area became members of the Fifth Regiment, Texas Infantry Volunteers that was involved with action in Galveston. The Fourth and Fifth Regiments of Hood’s Texas Brigade, each had a company of Texas volunteers from the Huntsville area.

In 1867, a yellow fever epidemic occurred, killing about ten percent of the population of Huntsville. In the same year, primary education was offered to Black children in Huntsville.

Walker County became one of three counties put under martial law during the Reconstruction Era. The murder of a freedman in January, 1871 led to several uprisings by citizens. A gunfight at the trial resulted and two members of the Texas State Police were wounded and two of the accused prisoners escaped. Only two citizens were willing to assist in the pursuit of the escaped men. There was an attempt to assassinate the judge involved. Martial law was imposed on February 15 for two months.

A rail link was opened in 1872 between Huntsville and the community of Phelps, Texas, where it connected to the Houston and Great Northern Railroad.

An institute for African-Americans was established in 1883. It was a coeducational facility founded by the Methodist Church and was called the Bishop Ward Normal and Collegiate Institute for Negroes.