The first landowner in Glen Ellyn was Deacon Winslow Churchill. He and his family moved to Glen Ellyn from New York in 1834. Other newcomers to the area built town necessities such as a tavern and school.
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.
In 1849, construction of a railroad line through Glen Ellyn was finished. The area around the railroad became the center of the town. At first, trains running through the town on the railway did not stop there. A local man named Lewey Q. Newton made an offer to the railroad company: Newton would build a depot and water tank out of his own pocket if the railroad would require trains to stop there. The depot that Newton built became known as Newtown Station.
The first church, a Congregational church, was built in 1862. Many Protestant churches were built in the village in the years to come. It wasn't until 60 years later that the first Catholic church was built.
In 1889, residents Thomas E. Hill and Philo Stacy spearheaded a project to create a new lake, called Lake Glen Ellyn, by having a damn built in a nearby stream. In 1890, residents discovered mineral springs near the village.
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.
The village's fire department was created in 1907. It would eventually become the last all-volunteer fire department in DuPage County by the end of the 1900s.
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 (named for three brothers that settled there), DuPage Center, Stacy's Corners (after the Stacy family), Newton's Station, Danby (after Danby, Vermont, a local landowner's birthplace), Prospect Park, and finally Glen Ellyn. The name Glen Ellyn is based on the Welsh version of the name of the then–village president Thomas E. Hill's wife Ellen, preceded by glen, referring to the local geography.