Daubert left the Reds late in the 1924 season after falling ill during a road trip to New York. Against his doctor's advice, he returned to play in the team's final home game of the season. On October 2, he had an appendectomy performed by Dr. Harry H. Hines, the Reds' team doctor. Complications from the operation arose, and a blood transfusion did not improve his health. He died one week after the operation in Cincinnati, with the doctor citing "exhaustion, resulting in indigestion, the immediate cause of death". It was later discovered that Daubert suffered from a hereditary blood disorder called hemolytic spherocytosis, which contributed to his death. He was interred at the Charles Baber Cemetery in Pottsville, Pennsylvania. Daubert was survived by his wife Gertrude, his son George, and his daughter Louisa. As of 2019, he remains the oldest ballplayer to die while in the majors.