The museum was founded by a group that included former Kansas City Monarchs outfielder Alfred 'Slick' Surratt, legendary first baseman and manager Buck O'Neil, researcher Larry Lester, historian Phil S. Dixon, and community leader Horace Peterson. It started in a single-room office inside the Lincoln Building at 18th and Vine, the intersection that once anchored Kansas City's black entertainment district. By 1994, the museum had expanded into a larger dedicated space. The early years were lean. By 2008, the NLBM was on the verge of financial collapse. Bob Kendrick took over as president in 2011 and led a turnaround rooted in community engagement. By 2012, the museum posted a profit of $300,000 -- its strongest year since 2007. In 2019, the American Business Awards recognized it as Nonprofit Organization of the Year.

The museum's centerpiece is an indoor baseball diamond adorned with bronze statues of twelve giants of the Negro leagues. Gibson, 'the Black Babe Ruth,' who allegedly hit over 80 home runs in a single season, crouches behind the plate. Buck Leonard, his teammate on the Homestead Grays, stands at first. John Henry Lloyd takes second, Judy Johnson mans shortstop, and Ray Dandridge holds third. The outfield belongs to Cool Papa Bell, Oscar Charleston, and Leon Day. At the plate is Martin Dihigo, the only player inducted into the Halls of Fame of three countries: Mexico, Cuba, and the United States. The statues also honor Rube Foster, who founded the first Negro National League in 1920, and Buck O'Neil, the former Kansas City Monarch who served on the museum's board until his death on October 6, 2006. O'Neil's Presidential Medal of Freedom, awarded posthumously by President George W. Bush, is now displayed in a special area dedicated to his memory.

The museum chronologically traces the Negro leagues from the founding of the Negro National League in 1920 through the Negro American League's final season in 1962. The walls are lined with photographs of players, owners, and officials. Game-worn uniforms, cleats, and gloves sit in lockers dedicated to the sport's greatest figures. The Kansas City Monarchs loom large in the story -- not only as one of the most successful franchises but as the team where Jackie Robinson played before breaking Major League Baseball's color barrier in 1947 with the Brooklyn Dodgers. In 2013, an advance screening of the film 42, the Robinson biographical movie, was held in Kansas City as a benefit for the museum. Harrison Ford, who portrayed Monarchs scout and Dodgers general manager Branch Rickey in the film, participated in the fundraiser.

On June 5, 2008, Rush bassist and vocalist Geddy Lee donated nearly 200 autographed baseballs to the museum -- one of the largest single donations the NLBM had ever received. The signatures include Hank Aaron, Cool Papa Bell, and Lionel Hampton. The gift was a reflection of the museum's reach beyond traditional baseball circles. Each year, the NLBM presents legacy awards named for Negro league greats: the Oscar Charleston Legacy Award for most valuable players, the Satchel Paige and Bullet Rogan Legacy Awards for pitchers, the Larry Doby Legacy Award for rookies, and the Jackie Robinson Lifetime Achievement Award for career excellence in the face of adversity. These awards tie the museum's mission directly to the present, honoring current Major League players while keeping alive the names and stories of those who played in baseball's shadow for four decades. The 18th & Vine District buzzes with that same spirit today -- jazz clubs, barbecue joints, and a museum that insists you remember the men who played the game when nobody was watching.