The village was first settled by Henry Chamberlain in 1850 and became a village in 1867. The village was originally called Chamberlain's Siding but was changed to Three Oaks. These oak trees were a guidepoint for train engineers. None of the original three oak trees remain today; the last was cut down nearly 100 years ago.
Three Oaks' hometown pride is evident during its Flag Day Celebration in June. The celebration and Flag Day Parade is the largest in the country.
Three Oaks celebrated the centennial of receiving the Dewey Cannon at the village's Flag Day Festival (June 9–11, 2000). A historical marker at Dewey Cannon Park in Three Oaks relates: "This cannon, captured in the Spanish-American War by Admiral Dewey, was presented to Three Oaks when its citizens raised fourteen hundred dollars for a memorial to the men of the battleship Maine. This was the largest contribution, per capita, of any community in the nation. 'Three Oaks Against the World', a local paper proudly boasted. This park was dedicated October 17, 1899, by President William McKinley, and others. Presentation of the cannon took place on June 28, 1900. Guest of honor was Helen Miller Gould, called the Spanish-American War's 'Florence Nightingale'. Thousands of people were in attendance on each occasion." The Dewey Cannon, which remains on display in the park of the same name, bears the engraved monogram of Queen Isabella II of Spain.
The Christmas movie Prancer, released in 1989, was filmed on location largely in the village of Three Oaks (other locations in nearby LaPorte, Indiana, were also used). A sequel, Prancer Returns, was made in 2001 (filming location Uxbridge, Ontario), in which a boy comes to Three Oaks to learn about the "Prancer incident".
Three Oaks is also home to the Warren Featherbone Factory, which was built over a century ago by Edward Kirk Warren to strip turkey feathers of their quills to use in women's garments of the era, such as corsets, which used "stiffeners". This replacement for the "whalebone" material was welcomed by the garment industry of the late 19th century. The factory still stands today and houses the Journeyman Distillery, Acorn Theater, and Featherbone Factory.
On November 4, 2008, the incumbent village councilors were voted out of office. The village faced bankruptcy in early December 2008 due to fiscal mismanagement and the State of Michigan took over financial management of the village with the appointment of a financial manager. The state of Michigan appointed Emergency Financial Manager Pam Amato in December 2008 to take over village operations and guide the newly elected Council through development of a five-year deficit elimination plan. The state approved that plan in August. Amato's term was completed in 2009. In February 2010, the Village of Three Oaks hired Patrick Yoder to serve as the first Village Manager.