Crown Hill National Cemetery is Sections 9 and 10 located within Crown Hill Cemetery. The national cemetery is comprised of 1.4 acres, and the property was purchased by the U.S. Government in 1866 for the purpose of reburying 707 Union soldiers from the City Cemetery. Those graves were originally marked by headboards, painted and lettered, which were later replaced with upright marble headstones. A bronze plaque on the grounds identifies the national cemetery and a commemorative monument stands within the Crown Hill National Cemetery section. There are 2,135 soldiers representing every war in which the United States has participated, with the last one being made in 1969 for Maj. Robert W. Hayes, an Air Force pilot killed in Vietnam. This cemetery is closed to new interments. However, space may be available in the same gravesite for eligible family members.

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Crown Hill National Cemetery is located 2.8 miles northwest of downtown Indianapolis, Ind., within the private Crown Hill Cemetery. During the Civil War, Union soldiers who died while stationed at the various camps near Indianapolis and at local hospitals were originally buried at nearby Green Lawn Cemetery. However, concern over the limited acreage and poor maintenance of these facilities led the governor to request a national cemetery for the city. The Federal government purchased lots within the new Crown Hill Cemetery (established in 1863) and in 1866, the remains buried at Green Lawn were reinterred at Crown Hill in a ceremony attended by James A. Ekin, the deputy quartermaster general. Today, the private Crown Hill is notable as the third-largest non-government cemetery in America.

In addition to the Union soldiers, Confederate prisoners were buried at Crown Hill National Cemetery. During the Civil War there were typically more than 3,500 Confederates held prisoner at Camp Morton on the north side of Indianapolis. Originally, the principle mustering, recruiting, and encampment site for many Hoosier regiments. After the fall of Forts Donelson and Henry in early 1862, thousands of captured Confederates were sent north to POW camps such as Camp Morton (others included Camp Butler in Springfield, Ill.; Camp Chase in Columbus, Ohio; and Camp Douglas in Chicago). About 15,000 prisoners occupied Camp Morton between 1862 and 1865. Typical of most prison facilities at that time, Camp Morton was unprepared for the large influx of prisoners. Medical care, food, and sanitary conditions were inadequate. Between 1862 and 1865, more than 1,700 Confederate deaths at Camp Morton resulted. Still, the death rates at Camp Morton were lower than most Northern prisons.

After it became the city's responsibility to find an acceptable burial ground for the Southern dead, a section of the Green Lawn cemetery was turned over to the government for burials. After the war, this land was sold to the railroad, and the remains removed to a mass grave in Section 32 of Crown Hill Cemetery. In 1989, two Indianapolis police officers initiated an effort to mark the graves of the Confederate POWs; other groups and individuals joined in, and in 1993 the new Confederate Memorial was dedicated. Crown Hill National Cemetery, including the national cemetery tract, was listed on the National Register of Historic Places in 1973.