The town had originally been in Walker County. When San Jacinto County was formed in 1870, the community was split east and west by the new county line. James W. Winters, former Alabaman, settled in the area just a year before Texas Independence in 1835. Other families moved into the area and by 1852, the community had promising population of 300 people.
Just before the Civil War Waverly was platted and incorporated. The town ( like Ivanhoe in North Texas) is said to be named after the writings of Sir Walter Scott. A male and female academy opened in 1856 and the town had a post office in operation from 1855 through 1872.
Storekeeper Meyer Levy, a Polish Jew and Civil War Veteran, suggested to others in the community that bringing new settlers from Poland would benefit all concerned. The Waverly Emigration Society was formed, but while the plan was to recruit about 150 workers; the numbers fell dramatically short of the goal. As the Houston and Great Northern Railroad extended it's tracks north through the region, fearful townspeople refused to grant a right-of-way to the railroad. This misguided refusal spawned the town of "New" Waverly 10 miles west and spelled the end to Waverly - which was thereafter referred to as Old Waverly.