By the first 20 years of the 20th century, professional baseball teams had been organized in every area of West Virginia. The earliest city to have a team was Wheeling, which played its first game in August 1866 on Wheeling Island Commons as the Hunkidori Base Ball Club, losing 45-12 to a team from Washington, Pennsylvania. Future major leaguers Jesse Burkett and Jack Glasscock emerged from Wheeling’s sandlots. Wheeling later had teams in the Class B Central League from 1903 through 1924. White semi-pro teams from Wheeling also hosted regular games against the great Homestead Grays teams that belonged to the First National Negro League. In 1933, Wheeling hosted the second, and final, game of the Second National Negro League championship between the Pittsburgh Crawfords and Chicago American Giants in an abbreviated series.

Fairmont, Clarksburg, and Piedmont played in the Class D Western Pennsylvania League in 1907. When the league folded a year later, Fairmont and Clarksburg switched to the Class D Pennsylvania-West Virginia League. Mannington spent less than half a season in professional ball, combining with Fairmont, Clarksburg, and Grafton to form the Class D West Virginia League in 1910. When the Grafton team disbanded on July 5, the league folded. Those early teams, which consisted mostly of local players, were not associated with the major leagues.

By 1920, 14 West Virginia cities and towns had spent time in professional baseball. They were Charleston, Clarksburg, Fairmont, Follansbee, Grafton, Huntington, Mannington, Martinsburg, Montgomery, Parkersburg, Piedmont, Point Pleasant, Wheeling, and Williamson. By the early 1930s, there were 11 teams, at Beckley, Bluefield, Charleston, Clarksburg, Fairmont, Huntington, Logan, Parkersburg, Welch, Wheeling, and Williamson.

In the early 1920s, future Hall of Fame members Hack Wilson and Lefty Grove played for Martinsburg of the Class D Blue Ridge League. In June 1920, Martinsburg famously traded Grove to the minor league Baltimore Orioles for $3,500, the cost of replacing its outfield fence, which had blown down during a storm. Five years later, the Orioles sold him to the Philadelphia A’s of the American League for $100,600. Martinsburg’s trade of Grove is often listed among the worst, and strangest, in baseball history. In 1934, Frank McCormick, who would become the 1940 National League Most Valuable Player, played for the Beckley Black Knights, a minor league affiliate of the Cincinnati Reds. In 1938-39, Stan Musial played for Williamson of the Class D Mountain State League. The minor league boom of the late 1940s largely bypassed West Virginia. At that time, only Charleston, Bluefield, and Welch fielded teams.

Charleston entered professional baseball in 1910, calling its team the Statesmen. The Statesmen played in the Class D Virginia Valley League with Huntington, Point Pleasant, Parkersburg, Montgomery, and Ashland-Catlettsburg (Kentucky). It was the start of a busy and productive century of baseball in the capital city. After one year in the Virginia Valley League, Charleston participated in the Class D Mountain State League (1911-12) and the Class D Ohio State League (1913-16). In 1916, the city built Kanawha Park, a 3,500-seat wooden structure on the site of what later became Watt Powell Park, but spent the next 15 years without a pro team. In 1931, Charleston joined the Class C Middle Atlantic League (1931-42), a 12-city affiliation that included Beckley, Huntington, Fairmont, Clarksburg, and Wheeling.

By 1936, Charleston and Huntington were the Middle Atlantic League's lone remaining West Virginia cities. That year, Huntington's Walter Alston, a future Hall of Fame manager, led the league with 35 home runs. Huntington dropped out after the '36 season, leaving Charleston as the league's only state representative. The other West Virginia cities offering professional baseball on the eve of World War II were Bluefield, Logan, Welch, and Williamson of the Class D Mountain State League.

Beginning with construction of 5,000-seat Watt Powell Park in 1949, Charleston began moving up the baseball ladder to the Class A Central League (1949-51), Class AAA American Association (1952-60), Class A Eastern League (1962-64), and Class AAA International League (1961, 1971-83). Charleston's move to the American Association in 1952—the highest level ever for a West Virginia city—happened suddenly and unexpectedly. On June 23 of that year, the Toledo Mud Hens moved to the West Virginia capital, thereby thrusting Charleston into competition with Milwaukee, Kansas City, St. Paul, Louisville, Indianapolis, Minneapolis, and Columbus. As a member of the American Association in 1956, Charleston produced the first of only two future Hall of Fame players in the city's long baseball history. Jim Bunning pitched for the team for three months before going to the Detroit Tigers.

After three years with no baseball (1984-86), the professional game returned to Charleston in 1987 as part of the Class A South Atlantic League (1987-2020); during these years, the team was known as the Charleston Wheelers (1987-94), Charleston Alley Cats (1995-2004), and West Virginia Power (2005-20). Charleston’s second future Hall of Fame player was reliever Trevor Hoffman, part of the Wheelers’ 1991 team. He initially was a third baseman and shortstop. Charleston manager and West Virginia native Jim Lett moved the below-average hitter and fielder to the pitcher’s mound. In the major leagues, Hoffman would become the first reliever to reach the 500- and 600-save levels. He was elected to the Hall of Fame in 2018. The National League reliever of the year award is named in his honor.

On April 14, 2005, Charleston opened a new baseball facility, Appalachian Power Park (now GoMart Ballpark), to replace Watt Powell Park.

By 2015, only Charleston, Bluefield, and Princeton had professional teams. Bluefield thrived as a member of the Appalachian Rookie League from 1946 to 2020 (with a one-year absence in 1956). The team produced major-league stars Cal Ripken Jr. and Eddie Murray. Nearby Princeton joined the league in 1988, its Rays offering the Bluefield Blue Jays some cross-county competition. Huntington had a rookie team, the Cubs, from 1990 to 1994. The team, a Chicago Cubs affiliate, competed against Bluefield and Princeton and others in the Appalachian League.

In 2015, the West Virginia Black Bears, a Pittsburgh Pirates affiliate, began playing at the new Monongalia County Ballpark as a member of the short-season New York-Penn League. In February 2021, Major League Baseball reorganized its minor league franchises, eliminating affiliations with the Power and two other West Virginia teams. The Princeton WhistlePigs and Bluefield Ridge Runners became part of the revamped Appalachian League for rising freshmen and sophomore college players; Princeton's team ceased operations after the 2023 season. The Black Bears are part of the MLB Draft League, an amateur league for draft-eligible prospects.

In February 2021 the owners of the West Virginia Power merged with the Lexington Legends ballclub, and the Power became the eighth member of the Atlantic League. In September 2021, the Power changed its name to the Charleston Dirty Birds.

In November 2023, the Appalachian League announced that minor league baseball would return to Huntington for the first time since 1994. Beginning in summer 2024, the Huntington Tri-State Coal Cats will play home games at the newly built Jack Cook Field.