"The Nation's Distinguished Jurist and Fort Smith's Beloved Citizen is no More."
- Fort Smith News Record, November 17, 1896
In 1889 and 1890 Judge Parker had the opportunity to take different positions within the federal judiciary; either position would have provided the judge with a reduced caseload. However, Parker had established himself in Fort Smith, and removed his name from consideration for the two positions.
The Courts Act of 1889, coming a month after Congress authorized the Supreme Court review, established a federal court system in the Indian Territory, further decreasing the Fort Smith court's jurisdiction.
The restrictions of the court's once vast jurisdiction were a source of frustration, but what bothered Judge Parker the most were the Supreme Court reversals of capital crimes tried in Fort Smith. Fully two-thirds of the cases appealed to the higher court were reversed and sent back to Fort Smith for new trials. In 1894 Judge Parker gained national attention in a dispute with the Supreme court over the case of Lafayette Hudson.
In 1895 a new Courts Act was passed which would remove the last remaining Indian Territory jurisdiction of the court effective September 1, 1896. Following the escape attempt of Cherokee Bill in the summer of 1895, which resulted in the death of a jail guard, Judge Parker again came into conflict with his superior when he blamed the Justice Department and the Supreme court for the incident. In the spring of 1896 a very public argument was carried on between Judge Parker and the Assistant Attorney General.
When the August term 1896 began, Judge Parker was at home, too sick to preside over the court. Twenty years of overwork had contributed to a variety of ailments, including Bright's Disease. When the jurisdiction of the court over lands in the Indian Territory came to an end on September 1, 1896, Parker had to be interviewed by reporters at his bedside. Scarcely two months after the jurisdictional change took effect, Judge Isaac C. Parker died on November 17, 1896. With his death, an era came to end at Fort Smith.