Maker's Mark's origin began when T. William Bill Samuels Sr., purchased the Burks' Distillery in Loretto, Kentucky, for $35,000 on October 1, 1953. Production began in 1954, and the first run was bottled in 1958 under the brand's distinctive dipped red wax seal (U.S. trademark serial number 73526578).

In the 1960s and 1970s, Maker's Mark was widely marketed with the tag line, It tastes expensive ... and is.

The distillery was listed on the National Register of Historic Places on December 31, 1974, and designated a National Historic Landmark on December 16, 1980, listed as Burks' Distillery, the first distillery in America to be recognized while the landmark buildings were in active production.

Maker's Mark was sold to Hiram Walker & Sons in 1981, which was acquired by the distillery giant Allied Domecq in 1987. When Allied-Domecq was bought by Pernod Ricard in 2005 the Maker's Mark was sold brand to Deerfield, Illinois-based Fortune Brands. Fortune Brands split in 2011, with its alcoholic beverage business becoming Beam Inc.

After the brand's creation by Bill Samuels, Sr., its production was overseen by his son Bill Samuels, Jr. until 2011 when he announced his retirement as president and CEO of Maker's Mark at the age of 70. His son Rob Samuels succeeded him in April 2011.

On February 9, 2013, the company sent a mass e-mail announcing a plan to reduce the alcohol strength of the whiskey, citing supply issues as the reason for the change. The result of this change would have been to reduce the product from 90 U.S. proof (45% alcohol by volume) to 84 U.S. proof (42% abv), which would have stretched inventory by about 6%. Maker's Mark said that their own tasting panel of distillery employees reported no taste difference in the lower proof, while industry analysts said that the difference would be subtle, and since most drinkers mix the bourbon or serve it on ice, few would be able to notice it. According to Neil Irwin for The Washington Post's Wonkblog, the decision can be explained by Beam's desire to keep Maker's Mark competitive as a premium bourbon at mid-range bars, and a well drink among high-end bars.

On February 17, the company said that it had reconsidered its decision after receiving a strong negative reaction from customers, and that it would continue to bottle at the original strength. Some overseas markets like Australia will continue to sell the whiskey at 40%.

In January 2014, Beam Inc announced its sale to Suntory Holdings, creating the third largest distilled spirits maker in the world. News of the proposed sale included bourbon executives vowing the product taste won't change – and neither will the company's historic purity standards.

In 2014, Maker's Mark released a Maker's Mark Cask Strength Bourbon in limited quantities initially available to consumers only at their distillery gift shop. ABV fluctuates each batch between 53% and 58%. The product was released on the global market in July 2016.

In November 2015 Suntory announced a major expansion of its distillery.