Much of the early collection amassed by the museum was destroyed in the Great Chicago Fire in 1871, but like the city, the museum rose from the ashes. Among its many documents which were lost in the fire was the original Emancipation Proclamation signed by Abraham Lincoln. After the fire, the Society began collecting new materials, which were stored in the Scammon Building until it, and their collection, were again destroyed by fire in 1874. The Chicago Historical Society built a fireproof building on the site of its pre-1871 building. The replacement building opened in 1896. The current home of the Museum was constructed in 1932, twelve years after the society purchased the large collection of Charles F. Gunther. In addition to the exhibits, the museum houses a research library which is open to the public.
On January 19 2006, the first passenger car to operate on the Chicago 'L' system in 1893 was transported to its new display location at the Chicago Historical Society. Passengers were allowed to ride the 1893 'L' from the Loop to Hyde Park station for 5 cents to attend the World's Columbian Exposition upon the line's opening. The car, known as CTA 1, was cosmetically restored into its 1893 appearance before being transported to the museum where it was lifted and inserted into an opening through the museum's second floor wall. The car's interior features include mahogany and rattan seats and etched glass windows. CTA 1 joins Pioneer, the first locomotive to operate in Chicago; a redesigned exhibit space to showcase the car and locomotive opened on September 30 2006.
The Museum also houses Chicago's most important collection of materials related to local history. It is open to the public, including high school students working on school projects, though the library holds short opening hours, amounting to less than 24 hours per week.