The constitution of West Virginia mandates a government divided into the legislative, executive, and judicial departments (Article V). The constitution vests the state's judicial power in a Supreme Court of Appeals and circuit courts and in the intermediate appellate courts and magistrate courts that the legislature might establish (Article VIII).

When West Virginia separated from Virginia, its court system mirrored that of the mother state. The Constitution of 1863 established the Supreme Court of Appeals, with three justices, and 11 circuit courts, and it provided several justices of the peace for every county. The justice of the peace courts were substantially the same as those established by Virginia in 1662. These courts decided minor civil controversies and acted as conservators of the peace until they were replaced by the magistrate courts in 1974. Besides the court structure, West Virginia also retained much of Virginia's system of laws. In fact, the Constitution of 1863 adopted Virginia common law and statutes as the law of West Virginia until such time as they were changed or repealed by the legislature. Some common law decisions made by Virginia courts are still part of the laws of the Mountain State.

The Constitution of 1872, now in force, increased the number of Supreme Court justices to four (now five) and strengthened the justices of the peace. The county commissioners, who replaced the township system of local government, had some judicial powers and commonly were referred to as the county court.

The most important modern event in the development of the West Virginia judiciary was the people's ratification of the Judicial Reorganization Amendment on November 5, 1974. It reorganized a court structure that had remained virtually the same since the attainment of statehood. The catalyst for judicial reform was in the decision State ex rel. Reece v. Giles, J. P. (1973), wherein the Supreme Court of Appeals held that the system of funding justice of the peace courts from fines was unconstitutional.

The amendment that followed replaced the justice of the peace courts with a system of magistrate courts, and gave the legislature the authority to establish a court of appeals between the circuit courts and the Supreme Court. Most importantly, the Judicial Reorganization Amendment created a modern unified court system, a simple, integrated hierarchy of courts. At its base is a magistrate court in each county; these courts process criminal misdemeanors and minor civil cases. Important litigation takes place in 31 circuit courts, which are the state's comprehensive general jurisdiction trial courts. These courts have jurisdiction in all criminal, civil, and juvenile matters. A constitutional amendment in 2000 established a separate family court system to make final decisions in divorce, annulment, child custody and other family law matters. There are 47 family court judges in 27 circuits. In 2021, the legislature created the Intermediate Court of Appeals, allowed by the 1974 amendment. It went into effect in 2022, establishing a three-judge panel serving 10-year staggered terms.

At the pinnacle of the system is the Supreme Court of Appeals, the court of last resort which must dispose of all petitions for appeal and decide those it chooses to hear. The court also serves as the administrative authority over the unified court system. In this capacity, it establishes procedural rules, determines policies for fiscal and staff management, supervises the caseload of the courts, and oversees the ethics for the bench and bar.

The Supreme Court accomplishes these responsibilities with the assistance of the administrative office of the courts. The director of the office is appointed by the court and serves as the administrative officer of the court system. This office also coordinates the training of circuit judges and magistrates. It encourages judges to seek training in such programs as the National Judicial College. It also conducts judicial training conferences that provide information on changes in state law and federal decisions that affect procedures, and reviews current trends in law, criminal sentencing, and other timely subjects. Most magistrates are not lawyers. Magistrates must attend classroom training and pass exams on law and procedure. West Virginia's training program for magistrates exceeds the training for non-lawyer judges provided by most states.

The Judicial Reorganization Amendment empowered the Supreme Court to promulgate rules. These rules govern people's access to the courts, how courts operate, the cost of using the courts, and the evidence and procedures allowed in litigation. Compared to other states, West Virginia's Supreme Court exercises considerable management over the courts.

The unified court system allows for centralized financial and personnel management. The administrative office oversees some aspects of personnel policy for nonjudicial personnel. It keeps statistics on the operations of all state courts, purchases their supplies and equipment, and gives other administrative assistance. The office also prepares the budget for all state courts. The constitution (Article VI, section 51) prevents the state legislature from decreasing any item in the budget submitted by the judiciary. A 1978 legislative attempt to decrease the judicial budget resulted in a lawsuit that confirmed the court's inherent power over the judiciary's budget (State ex rel. Bagley v. Blankenship, 1978).

The Supreme Court of Appeals, as the state's only appellate court, has an enormous workload. The court has complete discretion over its docket; citizens have no constitutional or statutory right to have any case or controversy reviewed by the court. The court must, as a practical matter, respond to significant political, social, and legal questions. As the number of appeals increased after 1960, the court moved from two annual sessions to meeting nearly continuously. It is among the busiest appellate courts in America.

In 2016, West Virginians began choosing their judges in nonpartisan elections; between elections, vacant judge positions are filled by appointment. The state's judges tend to keep in touch with the people and are aware of the practical significance of their decisions. Judges are participants in the political process. Although they have constraints on them not shared by members of the legislative and executive branches of government, judges make decisions of important political, social, and economic consequence.

For a number of important issues, the Supreme Court of Appeals is a noteworthy entity in West Virginia policy making. At times the court's decisions create new public policy or incrementally adjust existing policy. It is important to note, however, that in most of its cases the court engages in straightforward application of West Virginia statutes and common law. Innovations and changes made in public policy by the court play an important role in policy making, but are a small proportion of the court's decisions.

The court has made many important innovations in West Virginia law. For example, the court narrowed the immunity of employers from suits by injured workers (Mandolidis v. Elkins Industries, 1978), holding that workers' compensation coverage did not bar suit against intentional employer negligence. In Pauley v. Kelly (1979), the court ruled that unequal per-pupil funding among West Virginia counties violated the state constitution's mandate for a "thorough and efficient" school system. A complete restructuring of the prison system was required by the decision in Crain v. Bordenkircher (1986).

One of the most unusual events in West Virginia judicial history was the House of Delegates’ impeachment of all sitting Supreme Court of Appeals justices in 2018. It followed a controversy involving lavish remodeling and redecorating of court facilities and federal investigations of justices Allen Loughry and Menis Ketchum. Prior to the impeachment, Ketchum resigned and later plead guilty to one count of wire fraud, received probation, and had his law license annulled. After the remaining four justices were impeached in August 2018, Justice Robin Jean Davis retired from the bench to allow her seat to be filled in the November 2018 election. In the only actual trial, the State Senate voted 32-1-1 not to convict Justice Beth Walker. Five circuit court judges, temporarily serving as the Supreme Court of Appeals, blocked the Senate trial of Justice Margaret Workman on the grounds it violated the separation of powers doctrine; she remained on the court until her term expired at the end of 2020. Loughry was initially suspended and then resigned. He was later convicted in federal court on seven counts of wire fraud, one count of mail fraud, one count of witness tampering, and two counts of lying to the FBI; he served 20 months in prison.