The first Europeans known to have reached the area carved their names on beech trees near the river around 1775. By 1778, settlers established McFadden's Station on the north bank of the Barren River.

Present-day Bowling Green developed from homesteads erected by Robert and George Moore and General Elijah Covington, the namesake of the town near Cincinnati.^{[citation needed]} The Moore brothers arrived from Virginia circa 1794. In 1798, two years after Warren County had been formed, Robert Moore donated 2 acres (8,100 m²) of land to county trustees for the purpose of constructing public buildings. Soon after, he donated an additional 30 to 40 acres (120,000 to 160,000 m²) surrounding the original plot. The city of Bowling Green was officially incorporated by the Commonwealth of Kentucky on March 6, 1798.

Some controversy exists over the source of the town's name. The city refers to the first county commissioners' meeting (1798), which named the town "Bolin Green" after the Bowling Green in New York City, where patriots had pulled down a statue of King George III and used the lead to make bullets during the American Revolution. According to the Encyclopedia of Kentucky, the name was derived from Bowling Green, Virginia, from where early migrants had come, or the personal "ball alley game" of founder Robert Moore. Early records indicate that the city name was also spelled "Bowlingreen".

By 1810, Bowling Green had 154 residents. Growth in steamboat commerce and the proximity of the Barren River increased Bowling Green's prominence. Canal locks and dams on the Barren River made it much more navigable. In 1832, the first portage railway connected the river to the location of the current county courthouse. Mules pulled freight and passengers to and from the city on the tracks.

Despite rapid urbanization of the Bowling Green area in the 1830s, agriculture remained an important part of local life. A visitor to Bowling Green noted the boasting of a tavern proprietor named Benjamin Vance:

In 1859, the Louisville and Nashville Railroad (currently CSX Transportation) laid railroad through Bowling Green that connected the city with northern and southern markets.

Bowling Green declared itself neutral in an attempt to escape the Civil War. Because of its prime location and resources, however, both the Union and Confederacy sought control of the city. The majority of its residents rejected both the Confederacy and the Lincoln administration. On September 18, 1861, around 1300 Confederate soldiers arrived from Tennessee to occupy the city, placed under command of Kentucky native General Simon Bolivar Buckner. The city's pro-Union feelings surprised the Confederate occupiers. The Confederates fortified surrounding hills to secure possible military approaches to the valuable river and railroad assets. In November 1861, the provisional Confederate government of Kentucky chose Bowling Green as its capital.

On February 14, 1862, after receiving reports that Fort Henry on the Tennessee River and Fort Donelson on the Cumberland River had both been captured by Union forces under Ulysses S. Grant, the Confederates began to withdraw from Bowling Green. They destroyed bridges across the Barren River, the railroad depot, and other important buildings that could be used by the enemy. The city was subject to disruptions and raids throughout the remainder of the war. During the summer of 1864, Union General Stephen G. Burbridge arrested 22 civilians in and around Bowling Green on a charge of treason. This incident and other harsh treatment by federal authorities led to bitterness toward the Union among Bowling Green residents and increased sympathies with the Confederacy.

After the Civil War, Bowling Green's business district grew considerably. Previously, agriculture had dominated the city's economy. During the 1870s, many of the historic business structures seen today were erected. One of the most important businesses in Bowling Green of this era was Carie Burnam Taylor's dress-making company. By 1906, Taylor employed more than 200 women.

In 1868, the city constructed its first waterworks system. The fourth county courthouse was completed in 1868. The first three were completed in 1798, 1805, and 1813. In 1889, the first mule-drawn street cars appeared in the city. The first electric street cars began to replace them by 1895.

The Sisters of Charity of Nazareth founded St. Columbia's Academy in 1862, succeeded by St. Joseph's School in 1911. In 1884, the Southern Normal School, which had been founded in 1875, moved to Bowling Green from the town of Glasgow, Kentucky. Pleasant J. Potter founded a women's college in Bowling Green in 1889. It closed in 1909 and its property was sold to the Western Kentucky State Normal School (see below, now known as Western Kentucky University). Other important schools in this era were Methodist Warren College, Ogden College (which also became a part of Western Kentucky University), and Green River Female College, a boarding school.

In 1906, Henry Hardin Cherry, the president and owner of Southern Normal School, donated the school to the state as the basis of the Western State Normal School. The school trained teachers for the expanding educational needs of the state. This institution is now known as Western Kentucky University and is the second-largest public university in the state, having recently surpassed the University of Louisville.

In 1906, Doctors Lillian H. South, J. N. McCormack, and A.T. McCormack opened St. Joseph Hospital to provide medical and nursing care to the residents and students in the area.

In 1925, the third and last Louisville and Nashville Railroad Station was opened. About 27 trains arrived daily at the depot. Intercity bus lines were also a popular form of travel. By the 1960s, railroad travel had dramatically declined in the face of competition from airlines and automobiles. The station has been adapted for use as a museum.

In 1940, a Union Underwear factory built in Bowling Green bolstered the city's economy significantly. During the 1960s, the city's population began to surpass that of Ashland, Paducah, and Newport.

Downtown streets became a bottleneck for traffic. In 1949, the U.S. Route 31W Bypass was opened to alleviate traffic problems, but it also drew off business from downtown. The bypass grew to become a business hotspot in Bowling Green. A 1954 advertisement exclaimed, "Your business can grow in the direction Bowling Green is growing – to the 31-W By-Pass".

By the 1960s, the face of shopping was changing completely from the downtown retail square to suburban shopping centers. Between May and November 1967, stores in Bowling Green Mall opened for business. Another advertisement said, "One-stop shopping. Just park , step out and shop. You'll find everything close at hand." Between September 1979 and September 1980, stores in the larger Greenwood Mall came on line. The city's limits began to stretch toward Interstate 65.

By the late 1960s, Interstate 65, which runs just to the east of Bowling Green, was completed. The Green River Parkway (now called the William H. Natcher Parkway), was completed in the 1970s to connect Bowling Green and Owensboro. These vital transportation arteries attracted many industries to Bowling Green.

In 1981, General Motors moved its Chevrolet Corvette assembly plant from St. Louis, Missouri, to Bowling Green. In the same year, the National Corvette Homecoming event was created: it is a large, annual gathering of Corvette owners, car parades, and related activities in Bowling Green. In 1994, the National Corvette Museum was constructed near the assembly plant.

In 1997, Bowling Green was designated a Tree City USA by the National Arbor Day Foundation.

In 2012, the city undertook a feasibility study on ways to revitalize the downtown Bowling Green area. The Downtown Redevelopment Authority was formed to plan redevelopment. Plans for the project incorporated Bowling Green's waterfront assets, as well as its historic center and streetscape around Fountain Square. It also proposed a new building for the Bowling Green Area Chamber of Commerce, construction of a Riverwalk Park where downtown borders the Barren River, creation of a new public park called Circus Square, and installation of a new retail area, the Fountain Square Market.

As of spring 2009, the new Chamber of Commerce, Riverwalk Park, and Circus Square have been completed. The Southern Kentucky Performing Arts Center, a facility for arts and education, broke ground in October 2009 and celebrated its opening night on March 10, 2012, with a concert by Vince Gill. Ground was broken for the Fountain Square Market in 2012.

In 2005, an effort was made to incorporate a Whitewater Park into the downtown Bowling Green riverfront at Weldon Peete Park. Due to the recession, the project was not funded.

In 2011, the Bowling Green Riverfront Foundation expanded its efforts to develop land on the opposite side of Barren River from Mitch McConnell Park (which is located alongside the U.S. 31-W Bypass and the riverbank, between Louisville Road and Old Louisville Road), upriver to Peete Park. The new plans include use of the adjacent river for white-water sports—the stretch of river includes rapids rated on the International Scale of River Difficulty between Class II and Class IV—as well as a mountain biking trail, a bicycle pump track, and a rock climbing area. Some of this facility will be located on a reclaimed landfill, which had served as Bowling Green's garbage dump for many years.

As of the census of 2010, 58,067 people and 22,735 households resided in the city. The population density was 1631.1 people per square mile (630.5/km²). The racial makeup of the city was 75.8% White, 13.9% African American, 0.3% Native American, 4.2% Asian, 0.2% Pacific Islander, 2.16% from other races, and 2.7% from two or more races. Hispanics or Latinos of any race were 6.5% of the population.

Of the 22,735 households, 24.6% had children under the age of 18 living with them, 33.1% were married couples living together, 14.1% had a female householder with no husband present, and 48.3% were not families. About 35.4% of all households were made up of individuals, and 19.7% had someone living alone who was 65 years of age or older. The average household size was 2.28, and the average family size was 2.99.

In the city, the population was spread out, with 20.1% under the age of 18, 28% from 15 to 24, 25.6% from 25 to 44, 18.8% from 45 to 64, and 10.6% who were 65 or older. The median age was 27.6 years. Females made up 51.7% of the population and males made up 48.3%.

The median income for a household in the city was $33,362, and for families was $45,287. Males had a median income of $35,000 versus $28,916 for females. The per capita income for the city was $19,302. About 19.4% of families and 27.7% of the population were below the poverty line, including 30.9% of those under age 18.