The station first opened in a local store as Waverly around 1843. Although the surrounding area was renamed Holtsville in 1860 when a post office opened, the station retained the name "Waverly" until the 1890s, when farmers complained about their shipments going to an upstate town named Waverly by mistake. Holtsville Station was rebuilt on May 13, 1912, only to be burned in another fire on January 4, 1914, and replaced again later the same year. South of the station was the northern terminus of the
Suffolk Traction Company's main trolley line, which was proposed to be extended to
Port Jefferson, New York, across a bridge over the tracks before the company went bankrupt in 1919. The station building was bulldozed in June 1962, but the station itself continued to operate until March 16, 1998, when it was closed due to low ridership. ==References==