On 29 May 1893, the exhumed body of Confederate President Jefferson Davis was mourned by over 60,000 people as it lay in state in the hall, before being moved to his final resting place in Hollywood Cemetery (Richmond, Virginia).

The old Howard Library building and a nearby property neighboring the Confederate Memorial Hall were then converted into the Ogden Museum of Southern Art by UNO.

In 2001 the UNO foundation announced its claims to the Confederate Memorial Hall building and initiated efforts to remove the museum from the premises.

As the case proceeded through the appellate processes, Governor Mike Foster intervened in the dispute and assisted in the drafting of a compromise between UNO and the museum that would allow Confederate Memorial Hall to remain in its historic building.

In August 2003, at Foster's direction, both parties agreed to drop pending lawsuits to the building in exchange for fulfillment of a compromise agreement.

Per the agreement, UNO is required to cede its title claims to the Confederate Memorial Hall museum's land and building in exchange for the construction of a connecting tunnel through the basement as was proposed in the 1997 plan.