Following the Civil War, Virginia sued West Virginia in the U.S. Supreme Court in the case known as Virginia v. West Virginia, seeking to reclaim Berkeley and Jefferson counties.

Shortly after Virginia's secession in May 1861, representatives from the northwest counties met in Wheeling and formed the Reorganized Government of Virginia, which remained loyal to the Union. The Reorganized Government soon authorized a referendum on whether to form a new state out of the northwest region. Voters there endorsed the concept, and a constitutional convention ensued. Article I, Section 2 of the resulting state constitution defined the proposed state's territory as including 44 named counties and four more (Pendleton, Hardy, Hampshire, and Morgan) if the voters in those counties chose to join the new state. If they did, then the counties of Berkeley, Jefferson, and Frederick would also, upon voter approval, be included in West Virginia.

A referendum on the constitution passed in April 1862, and the first four additional counties opted to go with West Virginia. No vote was taken at the time in Berkeley, Jefferson, and Frederick because they were controlled by the Confederacy. In May, the Reorganized Government gave its consent to the formation of the new state consisting of 48 counties plus Berkeley, Jefferson, and Frederick "whenever the voters of said counties" assented. Congress agreed to the creation of West Virginia in December 1862, conditioned on a constitutional change regarding the elimination of slavery. The approval law described the new state as embracing 48 named counties, not including Berkeley or Jefferson. Meanwhile, on May 28, 1863, elections in Berkeley and Jefferson counties endorsed joining West Virginia, and those counties were included when statehood became official on June 20, 1863.

In December 1865, the Virginia legislature, now back in the hands of Old Virginia easterners, repealed its laws consenting to the admission of Berkeley and Jefferson counties into West Virginia. Then Virginia took the matter to the U.S. Supreme Court. Virginia argued that when Congress approved statehood for West Virginia, those counties were not included, and the relevant statute made no mention of their later addition. Virginia also alleged that the Berkeley and Jefferson votes to join West Virginia were fraudulent and void.

In Virginia v. West Virginia, the Supreme Court in 1871 rejected (6-3) Virginia's claims. It held that the statutes of the Reorganized Government regarding Berkeley and Jefferson effectively created an agreement between the two states that the counties would become part of West Virginia "whenever" voters assented. Congress had validly approved, too. The application for statehood had been carefully considered, and Congress had made admission contingent on voter approval of the constitutional change regarding slavery. An inference therefore arose that Congress "intended to consent to the admission of the State with the contingent boundaries provided for in its constitution and in the statute of Virginia . . . and in so doing [Congress] necessarily consented to the agreement of those States on that subject." As for the county referendums, the Court concluded that the certification of the elections by Virginia's own governor was conclusive on their validity. The reference was to Governor Pierpont of Reorganized Virginia.

The Court did not directly address the constitutionality of West Virginia's statehood, even though its validity had been questioned. Nevertheless, the result in Virginia v. West Virginia implicitly settled the matter, for all practical purposes.