Deacon Winslow Churchill and family arrived from New York in 1834 to become the first landowners in the area that is now Glen Ellyn. Moses Stacy, a soldier in the War of 1812, arrived here in 1835. His inn, Stacy's Tavern, built in 1846 and his second home, was a halfway stop between Chicago and the Fox River Valley and a probable stop for Galena, Illinois stagecoaches on their way to Rockford, Illinois. Stacy's Tavern, now a historical monument, stands at what is now the intersection of Geneva Road and Main Street.
The nucleus of settlement shifted to the south when the railroad came through the village in 1849. Although no stop was planned for the area, Lewey Q. Newton deeded a right-of-way to the railroad and offered to build a depot and water tank at his own expense if it would permit a stop there. This became known as Newton Station. Within three years, the new postmaster named the town Danby after his birthplace in Vermont.
Religious services were conducted by circuit riders until the first Congregational church was established in 1862. Various Protestant churches rose in the village; it would be more than 60 years before Roman Catholics built St. Petronille and the Maryknoll Seminary.
In 1889, Thomas E. Hill and Philo Stacy arranged to dam the stream near town to form Lake Glen Ellyn, named for the glen where it rests and a Welsh spelling of Hill's wife's name, Ellen. The following year, nearby mineral springs were discovered.
In 1891, Glen Ellyn, advertised as Chicago's newest suburb and health resort, became the village's official name; it was incorporated on May 10, 1892. The large Lake Glen Ellyn Hotel opened in 1892, the same year much of the business district was destroyed by fire. Fourteen years later, the hotel was struck by lightning and burned to the ground.
In 1907, Glen Ellyn's first fire department was organized. By the end of the twentieth century, it was known as the last all-volunteer fire organization in DuPage County, Illinois. By World War I, Glen Oak Country Club served the Oak Park and Glen Ellyn communities, and in 1922 the first Glenbard high school was built.
The town went through several names, including Babcock's Grove, DuPage Center, Stacy's Corners, Newton's Station, Danby, Prospect Park, and finally Glen Ellyn.